diff --git a/conf/collection_index_klits/AmpliSeq CD Indexes Plate A..txt b/conf/collection_index_klits/AmpliSeq CD Indexes Plate A..txt
new file mode 100644
index 00000000..109c6a60
--- /dev/null
+++ b/conf/collection_index_klits/AmpliSeq CD Indexes Plate A..txt	
@@ -0,0 +1,225 @@
+[Version]
+1
+[Name]
+AmpliSeq CD Indexes Plate A
+[PlateExtension]
+amp384a
+[Settings]
+IndexOnly
+Adapter	CTGTCTCTTATACACATCT
+[I7]
+7005	GTGAATAT
+7006	ACAGGCGC
+7007	CATAGAGT
+7008	TGCGAGAC
+7015	TCTCTACT
+7016	CTCTCGTC
+7017	CCAAGTCT
+7018	TTGGACTC
+7023	GCAGAATT
+7024	ATGAGGCC
+7025	ACTAAGAT
+7026	GTCGGAGC
+[I5]
+5001	AGCGCTAG
+5002	GATATCGA
+5007	ACATAGCG
+5008	GTGCGATA
+5009	CCAACAGA
+5010	TTGGTGAG
+5013	AACCGCGG
+5014	GGTTATAA
+[IndexPlateLayout]
+A01	7005	5001
+A02	7015	5002
+A03	7006	5007
+A04	7007	5008
+A05	7016	5009
+A06	7008	5010
+A07	7018	5001
+A08	7023	5002
+A09	7017	5007
+A10	7025	5008
+A11	7024	5009
+A12	7026	5010
+B01	7006	5002
+B02	7016	5001
+B03	7005	5008
+B04	7008	5007
+B05	7015	5010
+B06	7007	5009
+B07	7017	5002
+B08	7024	5001
+B09	7018	5008
+B10	7026	5007
+B11	7023	5010
+B12	7025	5009
+C01	7016	5007
+C02	7008	5008
+C03	7015	5009
+C04	7006	5010
+C05	7007	5013
+C06	7005	5014
+C07	7024	5007
+C08	7026	5008
+C09	7023	5009
+C10	7017	5010
+C11	7025	5013
+C12	7018	5014
+D01	7015	5008
+D02	7007	5007
+D03	7016	5010
+D04	7005	5009
+D05	7008	5014
+D06	7006	5013
+D07	7023	5008
+D08	7025	5007
+D09	7024	5010
+D10	7018	5009
+D11	7026	5014
+D12	7017	5013
+E01	7017	5009
+E02	7025	5010
+E03	7018	5013
+E04	7023	5014
+E05	7026	5001
+E06	7024	5002
+E07	7006	5009
+E08	7007	5010
+E09	7005	5013
+E10	7015	5014
+E11	7008	5001
+E12	7016	5002
+F01	7018	5010
+F02	7026	5009
+F03	7017	5014
+F04	7024	5013
+F05	7025	5002
+F06	7023	5001
+F07	7005	5010
+F08	7008	5009
+F09	7006	5014
+F10	7016	5013
+F11	7007	5002
+F12	7015	5001
+G01	7026	5013
+G02	7024	5014
+G03	7025	5001
+G04	7018	5002
+G05	7023	5007
+G06	7017	5008
+G07	7008	5013
+G08	7016	5014
+G09	7007	5001
+G10	7005	5002
+G11	7015	5007
+G12	7006	5008
+H01	7025	5014
+H02	7023	5013
+H03	7026	5002
+H04	7017	5001
+H05	7024	5008
+H06	7018	5007
+H07	7007	5014
+H08	7015	5013
+H09	7008	5002
+H10	7006	5001
+H11	7016	5008
+H12	7005	5007
+[DefaultLayout_DualIndex]
+A01	A01
+B01	B01
+C01	C01
+D01	D01
+E01	E01
+F01	F01
+G01	G01
+H01	H01
+A02	A02
+B02	B02
+C02	C02
+D02	D02
+E02	E02
+F02	F02
+G02	G02
+H02	H02
+A03	A03
+B03	B03
+C03	C03
+D03	D03
+E03	E03
+F03	F03
+G03	G03
+H03	H03
+A04	A04
+B04	B04
+C04	C04
+D04	D04
+E04	E04
+F04	F04
+G04	G04
+H04	H04
+A05	A05
+B05	B05
+C05	C05
+D05	D05
+E05	E05
+F05	F05
+G05	G05
+H05	H05
+A06	A06
+B06	B06
+C06	C06
+D06	D06
+E06	E06
+F06	F06
+G06	G06
+H06	H06
+A07	A07
+B07	B07
+C07	C07
+D07	D07
+E07	E07
+F07	F07
+G07	G07
+H07	H07
+A08	A08
+B08	B08
+C08	C08
+D08	D08
+E08	E08
+F08	F08
+G08	G08
+H08	H08
+A09	A09
+B09	B09
+C09	C09
+D09	D09
+E09	E09
+F09	F09
+G09	G09
+H09	H09
+A10	A10
+B10	B10
+C10	C10
+D10	D10
+E10	E10
+F10	F10
+G10	G10
+H10	H10
+A11	A11
+B11	B11
+C11	C11
+D11	D11
+E11	E11
+F11	F11
+G11	G11
+H11	H11
+A12	A12
+B12	B12
+C12	C12
+D12	D12
+E12	E12
+F12	F12
+G12	G12
+H12	H12
\ No newline at end of file
diff --git a/conf/collection_index_klits/AmpliSeq CD Indexes Plate B.txt b/conf/collection_index_klits/AmpliSeq CD Indexes Plate B.txt
new file mode 100644
index 00000000..17052d46
--- /dev/null
+++ b/conf/collection_index_klits/AmpliSeq CD Indexes Plate B.txt	
@@ -0,0 +1,226 @@
+
+[Version]
+1
+[Name]
+AmpliSeq CD Indexes Plate B
+[PlateExtension]
+amp384b
+[Settings]
+IndexOnly
+Adapter	CTGTCTCTTATACACATCT
+[I7]
+7027	AGCCTCAT
+7028	GATTCTGC
+7029	TCGTAGTG
+7030	CTACGACA
+7035	ATGGCATG
+7036	GCAATGCA
+7039	CTTATCGG
+7040	TCCGCTAA
+7041	GATCTATC
+7042	AGCTCGCT
+7047	ACACTAAG
+7048	GTGTCGGA
+[I5]
+5001	AGCGCTAG
+5002	GATATCGA
+5007	ACATAGCG
+5008	GTGCGATA
+5009	CCAACAGA
+5010	TTGGTGAG
+5013	AACCGCGG
+5014	GGTTATAA
+[IndexPlateLayout]
+A01	7027	5001
+A02	7035	5002
+A03	7028	5007
+A04	7029	5008
+A05	7036	5009
+A06	7030	5010
+A07	7040	5001
+A08	7041	5002
+A09	7039	5007
+A10	7047	5008
+A11	7042	5009
+A12	7048	5010
+B01	7028	5002
+B02	7036	5001
+B03	7027	5008
+B04	7030	5007
+B05	7035	5010
+B06	7029	5009
+B07	7039	5002
+B08	7042	5001
+B09	7040	5008
+B10	7048	5007
+B11	7041	5010
+B12	7047	5009
+C01	7036	5007
+C02	7030	5008
+C03	7035	5009
+C04	7028	5010
+C05	7029	5013
+C06	7027	5014
+C07	7042	5007
+C08	7048	5008
+C09	7041	5009
+C10	7039	5010
+C11	7047	5013
+C12	7040	5014
+D01	7035	5008
+D02	7029	5007
+D03	7036	5010
+D04	7027	5009
+D05	7030	5014
+D06	7028	5013
+D07	7041	5008
+D08	7047	5007
+D09	7042	5010
+D10	7040	5009
+D11	7048	5014
+D12	7039	5013
+E01	7039	5009
+E02	7047	5010
+E03	7040	5013
+E04	7041	5014
+E05	7048	5001
+E06	7042	5002
+E07	7028	5009
+E08	7029	5010
+E09	7027	5013
+E10	7035	5014
+E11	7030	5001
+E12	7036	5002
+F01	7040	5010
+F02	7048	5009
+F03	7039	5014
+F04	7042	5013
+F05	7047	5002
+F06	7041	5001
+F07	7027	5010
+F08	7030	5009
+F09	7028	5014
+F10	7036	5013
+F11	7029	5002
+F12	7035	5001
+G01	7048	5013
+G02	7042	5014
+G03	7047	5001
+G04	7040	5002
+G05	7041	5007
+G06	7039	5008
+G07	7030	5013
+G08	7036	5014
+G09	7029	5001
+G10	7027	5002
+G11	7035	5007
+G12	7028	5008
+H01	7047	5014
+H02	7041	5013
+H03	7048	5002
+H04	7039	5001
+H05	7042	5008
+H06	7040	5007
+H07	7029	5014
+H08	7035	5013
+H09	7030	5002
+H10	7028	5001
+H11	7036	5008
+H12	7027	5007
+[DefaultLayout_DualIndex]
+A01	A01
+B01	B01
+C01	C01
+D01	D01
+E01	E01
+F01	F01
+G01	G01
+H01	H01
+A02	A02
+B02	B02
+C02	C02
+D02	D02
+E02	E02
+F02	F02
+G02	G02
+H02	H02
+A03	A03
+B03	B03
+C03	C03
+D03	D03
+E03	E03
+F03	F03
+G03	G03
+H03	H03
+A04	A04
+B04	B04
+C04	C04
+D04	D04
+E04	E04
+F04	F04
+G04	G04
+H04	H04
+A05	A05
+B05	B05
+C05	C05
+D05	D05
+E05	E05
+F05	F05
+G05	G05
+H05	H05
+A06	A06
+B06	B06
+C06	C06
+D06	D06
+E06	E06
+F06	F06
+G06	G06
+H06	H06
+A07	A07
+B07	B07
+C07	C07
+D07	D07
+E07	E07
+F07	F07
+G07	G07
+H07	H07
+A08	A08
+B08	B08
+C08	C08
+D08	D08
+E08	E08
+F08	F08
+G08	G08
+H08	H08
+A09	A09
+B09	B09
+C09	C09
+D09	D09
+E09	E09
+F09	F09
+G09	G09
+H09	H09
+A10	A10
+B10	B10
+C10	C10
+D10	D10
+E10	E10
+F10	F10
+G10	G10
+H10	H10
+A11	A11
+B11	B11
+C11	C11
+D11	D11
+E11	E11
+F11	F11
+G11	G11
+H11	H11
+A12	A12
+B12	B12
+C12	C12
+D12	D12
+E12	E12
+F12	F12
+G12	G12
+H12	H12
\ No newline at end of file
diff --git a/conf/collection_index_klits/AmpliSeq CD Indexes Plate C.txt b/conf/collection_index_klits/AmpliSeq CD Indexes Plate C.txt
new file mode 100644
index 00000000..8feeaf01
--- /dev/null
+++ b/conf/collection_index_klits/AmpliSeq CD Indexes Plate C.txt	
@@ -0,0 +1,225 @@
+[Version]
+1
+[Name]
+AmpliSeq CD Indexes Plate C
+[PlateExtension]
+amp384c
+[Settings]
+IndexOnly
+Adapter	CTGTCTCTTATACACATCT
+[I7]
+7005	GTGAATAT
+7006	ACAGGCGC
+7007	CATAGAGT
+7008	TGCGAGAC
+7015	TCTCTACT
+7016	CTCTCGTC
+7017	CCAAGTCT
+7018	TTGGACTC
+7023	GCAGAATT
+7024	ATGAGGCC
+7025	ACTAAGAT
+7026	GTCGGAGC
+[I5]
+5017	CTAGCTTG
+5018	TCGATCCA
+5025	ATACCAAG
+5026	GCGTTGGA
+5027	CTTCACGG
+5028	TCCTGTAA
+5031	CGCTCGTG
+5032	TATCTACA
+[IndexPlateLayout]
+A01	7005	5017
+A02	7015	5018
+A03	7006	5025
+A04	7007	5026
+A05	7016	5027
+A06	7008	5028
+A07	7018	5017
+A08	7023	5018
+A09	7017	5025
+A10	7025	5026
+A11	7024	5027
+A12	7026	5028
+B01	7006	5018
+B02	7016	5017
+B03	7005	5026
+B04	7008	5025
+B05	7015	5028
+B06	7007	5027
+B07	7017	5018
+B08	7024	5017
+B09	7018	5026
+B10	7026	5025
+B11	7023	5028
+B12	7025	5027
+C01	7016	5025
+C02	7008	5026
+C03	7015	5027
+C04	7006	5028
+C05	7007	5031
+C06	7005	5032
+C07	7024	5025
+C08	7026	5026
+C09	7023	5027
+C10	7017	5028
+C11	7025	5031
+C12	7018	5032
+D01	7015	5026
+D02	7007	5025
+D03	7016	5028
+D04	7005	5027
+D05	7008	5032
+D06	7006	5031
+D07	7023	5026
+D08	7025	5025
+D09	7024	5028
+D10	7018	5027
+D11	7026	5032
+D12	7017	5031
+E01	7017	5027
+E02	7025	5028
+E03	7018	5031
+E04	7023	5032
+E05	7026	5017
+E06	7024	5018
+E07	7006	5027
+E08	7007	5028
+E09	7005	5031
+E10	7015	5032
+E11	7008	5017
+E12	7016	5018
+F01	7018	5028
+F02	7026	5027
+F03	7017	5032
+F04	7024	5031
+F05	7025	5018
+F06	7023	5017
+F07	7005	5028
+F08	7008	5027
+F09	7006	5032
+F10	7016	5031
+F11	7007	5018
+F12	7015	5017
+G01	7026	5031
+G02	7024	5032
+G03	7025	5017
+G04	7018	5018
+G05	7023	5025
+G06	7017	5026
+G07	7008	5031
+G08	7016	5032
+G09	7007	5017
+G10	7005	5018
+G11	7015	5025
+G12	7006	5026
+H01	7025	5032
+H02	7023	5031
+H03	7026	5018
+H04	7017	5017
+H05	7024	5026
+H06	7018	5025
+H07	7007	5032
+H08	7015	5031
+H09	7008	5018
+H10	7006	5017
+H11	7016	5026
+H12	7005	5025
+[DefaultLayout_DualIndex]
+A01	A01
+B01	B01
+C01	C01
+D01	D01
+E01	E01
+F01	F01
+G01	G01
+H01	H01
+A02	A02
+B02	B02
+C02	C02
+D02	D02
+E02	E02
+F02	F02
+G02	G02
+H02	H02
+A03	A03
+B03	B03
+C03	C03
+D03	D03
+E03	E03
+F03	F03
+G03	G03
+H03	H03
+A04	A04
+B04	B04
+C04	C04
+D04	D04
+E04	E04
+F04	F04
+G04	G04
+H04	H04
+A05	A05
+B05	B05
+C05	C05
+D05	D05
+E05	E05
+F05	F05
+G05	G05
+H05	H05
+A06	A06
+B06	B06
+C06	C06
+D06	D06
+E06	E06
+F06	F06
+G06	G06
+H06	H06
+A07	A07
+B07	B07
+C07	C07
+D07	D07
+E07	E07
+F07	F07
+G07	G07
+H07	H07
+A08	A08
+B08	B08
+C08	C08
+D08	D08
+E08	E08
+F08	F08
+G08	G08
+H08	H08
+A09	A09
+B09	B09
+C09	C09
+D09	D09
+E09	E09
+F09	F09
+G09	G09
+H09	H09
+A10	A10
+B10	B10
+C10	C10
+D10	D10
+E10	E10
+F10	F10
+G10	G10
+H10	H10
+A11	A11
+B11	B11
+C11	C11
+D11	D11
+E11	E11
+F11	F11
+G11	G11
+H11	H11
+A12	A12
+B12	B12
+C12	C12
+D12	D12
+E12	E12
+F12	F12
+G12	G12
+H12	H12
\ No newline at end of file
diff --git a/conf/collection_index_klits/AmpliSeq CD Indexes Plate D.txt b/conf/collection_index_klits/AmpliSeq CD Indexes Plate D.txt
new file mode 100644
index 00000000..9b7414e6
--- /dev/null
+++ b/conf/collection_index_klits/AmpliSeq CD Indexes Plate D.txt	
@@ -0,0 +1,225 @@
+[Version]
+1
+[Name]
+AmpliSeq CD Indexes Plate D
+[PlateExtension]
+amp384d
+[Settings]
+IndexOnly
+Adapter	CTGTCTCTTATACACATCT
+[I7]
+7027	AGCCTCAT
+7028	GATTCTGC
+7029	TCGTAGTG
+7030	CTACGACA
+7035	ATGGCATG
+7036	GCAATGCA
+7039	CTTATCGG
+7040	TCCGCTAA
+7041	GATCTATC
+7042	AGCTCGCT
+7047	ACACTAAG
+7048	GTGTCGGA
+[I5]
+5017	CTAGCTTG
+5018	TCGATCCA
+5025	ATACCAAG
+5026	GCGTTGGA
+5027	CTTCACGG
+5028	TCCTGTAA
+5031	CGCTCGTG
+5032	TATCTACA
+[IndexPlateLayout]
+A01	7027	5017
+A02	7035	5018
+A03	7028	5025
+A04	7029	5026
+A05	7036	5027
+A06	7030	5028
+A07	7040	5017
+A08	7041	5018
+A09	7039	5025
+A10	7047	5026
+A11	7042	5027
+A12	7048	5028
+B01	7028	5018
+B02	7036	5017
+B03	7027	5026
+B04	7030	5025
+B05	7035	5028
+B06	7029	5027
+B07	7039	5018
+B08	7042	5017
+B09	7040	5026
+B10	7048	5025
+B11	7041	5028
+B12	7047	5027
+C01	7036	5025
+C02	7030	5026
+C03	7035	5027
+C04	7028	5028
+C05	7029	5031
+C06	7027	5032
+C07	7042	5025
+C08	7048	5026
+C09	7041	5027
+C10	7039	5028
+C11	7047	5031
+C12	7040	5032
+D01	7035	5026
+D02	7029	5025
+D03	7036	5028
+D04	7027	5027
+D05	7030	5032
+D06	7028	5031
+D07	7041	5026
+D08	7047	5025
+D09	7042	5028
+D10	7040	5027
+D11	7048	5032
+D12	7039	5031
+E01	7039	5027
+E02	7047	5028
+E03	7040	5031
+E04	7041	5032
+E05	7048	5017
+E06	7042	5018
+E07	7028	5027
+E08	7029	5028
+E09	7027	5031
+E10	7035	5032
+E11	7030	5017
+E12	7036	5018
+F01	7040	5028
+F02	7048	5027
+F03	7039	5032
+F04	7042	5031
+F05	7047	5018
+F06	7041	5017
+F07	7027	5028
+F08	7030	5027
+F09	7028	5032
+F10	7036	5031
+F11	7029	5018
+F12	7035	5017
+G01	7048	5031
+G02	7042	5032
+G03	7047	5017
+G04	7040	5018
+G05	7041	5025
+G06	7039	5026
+G07	7030	5031
+G08	7036	5032
+G09	7029	5017
+G10	7027	5018
+G11	7035	5025
+G12	7028	5026
+H01	7047	5032
+H02	7041	5031
+H03	7048	5018
+H04	7039	5017
+H05	7042	5026
+H06	7040	5025
+H07	7029	5032
+H08	7035	5031
+H09	7030	5018
+H10	7028	5017
+H11	7036	5026
+H12	7027	5025
+[DefaultLayout_DualIndex]
+A01	A01
+B01	B01
+C01	C01
+D01	D01
+E01	E01
+F01	F01
+G01	G01
+H01	H01
+A02	A02
+B02	B02
+C02	C02
+D02	D02
+E02	E02
+F02	F02
+G02	G02
+H02	H02
+A03	A03
+B03	B03
+C03	C03
+D03	D03
+E03	E03
+F03	F03
+G03	G03
+H03	H03
+A04	A04
+B04	B04
+C04	C04
+D04	D04
+E04	E04
+F04	F04
+G04	G04
+H04	H04
+A05	A05
+B05	B05
+C05	C05
+D05	D05
+E05	E05
+F05	F05
+G05	G05
+H05	H05
+A06	A06
+B06	B06
+C06	C06
+D06	D06
+E06	E06
+F06	F06
+G06	G06
+H06	H06
+A07	A07
+B07	B07
+C07	C07
+D07	D07
+E07	E07
+F07	F07
+G07	G07
+H07	H07
+A08	A08
+B08	B08
+C08	C08
+D08	D08
+E08	E08
+F08	F08
+G08	G08
+H08	H08
+A09	A09
+B09	B09
+C09	C09
+D09	D09
+E09	E09
+F09	F09
+G09	G09
+H09	H09
+A10	A10
+B10	B10
+C10	C10
+D10	D10
+E10	E10
+F10	F10
+G10	G10
+H10	H10
+A11	A11
+B11	B11
+C11	C11
+D11	D11
+E11	E11
+F11	F11
+G11	G11
+H11	H11
+A12	A12
+B12	B12
+C12	C12
+D12	D12
+E12	E12
+F12	F12
+G12	G12
+H12	H12
\ No newline at end of file
diff --git a/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set A.txt b/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set A.txt
new file mode 100644
index 00000000..8bcdf33f
--- /dev/null
+++ b/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set A.txt	
@@ -0,0 +1,494 @@
+[Version]
+1
+[Name]
+IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set A
+[PlateExtension]
+nexud384a
+[Settings]
+Adapter	CTGTCTCTTATACACATCT
+[I7]
+UDP0001	GAACTGAGCG
+UDP0002	AGGTCAGATA
+UDP0003	CGTCTCATAT
+UDP0004	ATTCCATAAG
+UDP0005	GACGAGATTA
+UDP0006	AACATCGCGC
+UDP0007	CTAGTGCTCT
+UDP0008	GATCAAGGCA
+UDP0009	GACTGAGTAG
+UDP0010	AGTCAGACGA
+UDP0011	CCGTATGTTC
+UDP0012	GAGTCATAGG
+UDP0013	CTTGCCATTA
+UDP0014	GAAGCGGCAC
+UDP0015	TCCATTGCCG
+UDP0016	CGGTTACGGC
+UDP0017	GAGAATGGTT
+UDP0018	AGAGGCAACC
+UDP0019	CCATCATTAG
+UDP0020	GATAGGCCGA
+UDP0021	ATGGTTGACT
+UDP0022	TATTGCGCTC
+UDP0023	ACGCCTTGTT
+UDP0024	TTCTACATAC
+UDP0025	AACCATAGAA
+UDP0026	GGTTGCGAGG
+UDP0027	TAAGCATCCA
+UDP0028	ACCACGACAT
+UDP0029	GCCGCACTCT
+UDP0030	CCACCAGGCA
+UDP0031	GTGACACGCA
+UDP0032	ACAGTGTATG
+UDP0033	TGATTATACG
+UDP0034	CAGCCGCGTA
+UDP0035	GGTAACTCGC
+UDP0036	ACCGGCCGTA
+UDP0037	TGTAATCGAC
+UDP0038	GTGCAGACAG
+UDP0039	CAATCGGCTG
+UDP0040	TATGTAGTCA
+UDP0041	ACTCGGCAAT
+UDP0042	GTCTAATGGC
+UDP0043	CCATCTCGCC
+UDP0044	CTGCGAGCCA
+UDP0045	CGTTATTCTA
+UDP0046	AGATCCATTA
+UDP0047	GTCCTGGATA
+UDP0048	CAGTGGCACT
+UDP0049	AGTGTTGCAC
+UDP0050	GACACCATGT
+UDP0051	CCTGTCTGTC
+UDP0052	TGATGTAAGA
+UDP0053	GGAATTGTAA
+UDP0054	GCATAAGCTT
+UDP0055	CTGAGGAATA
+UDP0056	AACGCACGAG
+UDP0057	TCTATCCTAA
+UDP0058	CTCGCTTCGG
+UDP0059	CTGTTGGTCC
+UDP0060	TTACCTGGAA
+UDP0061	TGGCTAATCA
+UDP0062	AACACTGTTA
+UDP0063	ATTGCGCGGT
+UDP0064	TGGCGCGAAC
+UDP0065	TAATGTGTCT
+UDP0066	ATACCAACGC
+UDP0067	AGGATGTGCT
+UDP0068	CACGGAACAA
+UDP0069	TGGAGTACTT
+UDP0070	GTATTGACGT
+UDP0071	CTTGTACACC
+UDP0072	ACACAGGTGG
+UDP0073	CCTGCGGAAC
+UDP0074	TTCATAAGGT
+UDP0075	CTCTGCAGCG
+UDP0076	CTGACTCTAC
+UDP0077	TCTGGTATCC
+UDP0078	CATTAGTGCG
+UDP0079	ACGGTCAGGA
+UDP0080	GGCAAGCCAG
+UDP0081	TGTCGCTGGT
+UDP0082	ACCGTTACAA
+UDP0083	TATGCCTTAC
+UDP0084	ACAAGTGGAC
+UDP0085	TGGTACCTAA
+UDP0086	TTGGAATTCC
+UDP0087	CCTCTACATG
+UDP0088	GGAGCGTGTA
+UDP0089	GTCCGTAAGC
+UDP0090	ACTTCAAGCG
+UDP0091	TCAGAAGGCG
+UDP0092	GCGTTGGTAT
+UDP0093	ACATATCCAG
+UDP0094	TCATAGATTG
+UDP0095	GTATTCCACC
+UDP0096	CCTCCGTCCA
+[I5]
+UDP0001	TCGTGGAGCG
+UDP0002	CTACAAGATA
+UDP0003	TATAGTAGCT
+UDP0004	TGCCTGGTGG
+UDP0005	ACATTATCCT
+UDP0006	GTCCACTTGT
+UDP0007	TGGAACAGTA
+UDP0008	CCTTGTTAAT
+UDP0009	GTTGATAGTG
+UDP0010	ACCAGCGACA
+UDP0011	CATACACTGT
+UDP0012	GTGTGGCGCT
+UDP0013	ATCACGAAGG
+UDP0014	CGGCTCTACT
+UDP0015	GAATGCACGA
+UDP0016	AAGACTATAG
+UDP0017	TCGGCAGCAA
+UDP0018	CTAATGATGG
+UDP0019	GGTTGCCTCT
+UDP0020	CGCACATGGC
+UDP0021	GGCCTGTCCT
+UDP0022	CTGTGTTAGG
+UDP0023	TAAGGAACGT
+UDP0024	CTAACTGTAA
+UDP0025	GGCGAGATGG
+UDP0026	AATAGAGCAA
+UDP0027	TCAATCCATT
+UDP0028	TCGTATGCGG
+UDP0029	TCCGACCTCG
+UDP0030	CTTATGGAAT
+UDP0031	GCTTACGGAC
+UDP0032	GAACATACGG
+UDP0033	GTCGATTACA
+UDP0034	ACTAGCCGTG
+UDP0035	AAGTTGGTGA
+UDP0036	TGGCAATATT
+UDP0037	GATCACCGCG
+UDP0038	TACCATCCGT
+UDP0039	GCTGTAGGAA
+UDP0040	CGCACTAATG
+UDP0041	GACAACTGAA
+UDP0042	AGTGGTCAGG
+UDP0043	TTCTATGGTT
+UDP0044	AATCCGGCCA
+UDP0045	CCATAAGGTT
+UDP0046	ATCTCTACCA
+UDP0047	CGGTGGCGAA
+UDP0048	TAACAATAGG
+UDP0049	CTGGTACACG
+UDP0050	TCAACGTGTA
+UDP0051	ACTGTTGTGA
+UDP0052	GTGCGTCCTT
+UDP0053	AGCACATCCT
+UDP0054	TTCCGTCGCA
+UDP0055	CTTAACCACT
+UDP0056	GCCTCGGATA
+UDP0057	CGTCGACTGG
+UDP0058	TACTAGTCAA
+UDP0059	ATAGACCGTT
+UDP0060	ACAGTTCCAG
+UDP0061	AGGCATGTAG
+UDP0062	GCAAGTCTCA
+UDP0063	TTGGCTCCGC
+UDP0064	AACTGATACT
+UDP0065	GTAAGGCATA
+UDP0066	AATTGCTGCG
+UDP0067	TTACAATTCC
+UDP0068	AACCTAGCAC
+UDP0069	TCTGTGTGGA
+UDP0070	GGAATTCCAA
+UDP0071	AAGCGCGCTT
+UDP0072	TGAGCGTTGT
+UDP0073	ATCATAGGCT
+UDP0074	TGTTAGAAGG
+UDP0075	GATGGATGTA
+UDP0076	ACGGCCGTCA
+UDP0077	CGTTGCTTAC
+UDP0078	TGACTACATA
+UDP0079	CGGCCTCGTT
+UDP0080	CAAGCATCCG
+UDP0081	TCGTCTGACT
+UDP0082	CTCATAGCGA
+UDP0083	AGACACATTA
+UDP0084	GCGCGATGTT
+UDP0085	CATGAGTACT
+UDP0086	ACGTCAATAC
+UDP0087	GATACCTCCT
+UDP0088	ATCCGTAAGT
+UDP0089	CGTGTATCTT
+UDP0090	GAACCATGAA
+UDP0091	GGCCATCATA
+UDP0092	ACATACTTCC
+UDP0093	TATGTGCAAT
+UDP0094	GATTAAGGTG
+UDP0095	ATGTAGACAA
+UDP0096	CACATCGGTG
+
+[IndexPlateLayout]
+A01	UDP0001	UDP0001
+B01	UDP0002	UDP0002
+C01	UDP0003	UDP0003
+D01	UDP0004	UDP0004
+E01	UDP0005	UDP0005
+F01	UDP0006	UDP0006
+G01	UDP0007	UDP0007
+H01	UDP0008	UDP0008
+A02	UDP0009	UDP0009
+B02	UDP0010	UDP0010
+C02	UDP0011	UDP0011
+D02	UDP0012	UDP0012
+E02	UDP0013	UDP0013
+F02	UDP0014	UDP0014
+G02	UDP0015	UDP0015
+H02	UDP0016	UDP0016
+A03	UDP0017	UDP0017
+B03	UDP0018	UDP0018
+C03	UDP0019	UDP0019
+D03	UDP0020	UDP0020
+E03	UDP0021	UDP0021
+F03	UDP0022	UDP0022
+G03	UDP0023	UDP0023
+H03	UDP0024	UDP0024
+A04	UDP0025	UDP0025
+B04	UDP0026	UDP0026
+C04	UDP0027	UDP0027
+D04	UDP0028	UDP0028
+E04	UDP0029	UDP0029
+F04	UDP0030	UDP0030
+G04	UDP0031	UDP0031
+H04	UDP0032	UDP0032
+A05	UDP0033	UDP0033
+B05	UDP0034	UDP0034
+C05	UDP0035	UDP0035
+D05	UDP0036	UDP0036
+E05	UDP0037	UDP0037
+F05	UDP0038	UDP0038
+G05	UDP0039	UDP0039
+H05	UDP0040	UDP0040
+A06	UDP0041	UDP0041
+B06	UDP0042	UDP0042
+C06	UDP0043	UDP0043
+D06	UDP0044	UDP0044
+E06	UDP0045	UDP0045
+F06	UDP0046	UDP0046
+G06	UDP0047	UDP0047
+H06	UDP0048	UDP0048
+A07	UDP0049	UDP0049
+B07	UDP0050	UDP0050
+C07	UDP0051	UDP0051
+D07	UDP0052	UDP0052
+E07	UDP0053	UDP0053
+F07	UDP0054	UDP0054
+G07	UDP0055	UDP0055
+H07	UDP0056	UDP0056
+A08	UDP0057	UDP0057
+B08	UDP0058	UDP0058
+C08	UDP0059	UDP0059
+D08	UDP0060	UDP0060
+E08	UDP0061	UDP0061
+F08	UDP0062	UDP0062
+G08	UDP0063	UDP0063
+H08	UDP0064	UDP0064
+A09	UDP0065	UDP0065
+B09	UDP0066	UDP0066
+C09	UDP0067	UDP0067
+D09	UDP0068	UDP0068
+E09	UDP0069	UDP0069
+F09	UDP0070	UDP0070
+G09	UDP0071	UDP0071
+H09	UDP0072	UDP0072
+A10	UDP0073	UDP0073
+B10	UDP0074	UDP0074
+C10	UDP0075	UDP0075
+D10	UDP0076	UDP0076
+E10	UDP0077	UDP0077
+F10	UDP0078	UDP0078
+G10	UDP0079	UDP0079
+H10	UDP0080	UDP0080
+A11	UDP0081	UDP0081
+B11	UDP0082	UDP0082
+C11	UDP0083	UDP0083
+D11	UDP0084	UDP0084
+E11	UDP0085	UDP0085
+F11	UDP0086	UDP0086
+G11	UDP0087	UDP0087
+H11	UDP0088	UDP0088
+A12	UDP0089	UDP0089
+B12	UDP0090	UDP0090
+C12	UDP0091	UDP0091
+D12	UDP0092	UDP0092
+E12	UDP0093	UDP0093
+F12	UDP0094	UDP0094
+G12	UDP0095	UDP0095
+H12	UDP0096	UDP0096
+[DefaultLayout_SingleIndex]
+A01	A01
+B01	B01
+C01	C01
+D01	D01
+E01	E01
+F01	F01
+G01	G01
+H01	H01
+A02	A02
+B02	B02
+C02	C02
+D02	D02
+E02	E02
+F02	F02
+G02	G02
+H02	H02
+A03	A03
+B03	B03
+C03	C03
+D03	D03
+E03	E03
+F03	F03
+G03	G03
+H03	H03
+A04	A04
+B04	B04
+C04	C04
+D04	D04
+E04	E04
+F04	F04
+G04	G04
+H04	H04
+A05	A05
+B05	B05
+C05	C05
+D05	D05
+E05	E05
+F05	F05
+G05	G05
+H05	H05
+A06	A06
+B06	B06
+C06	C06
+D06	D06
+E06	E06
+F06	F06
+G06	G06
+H06	H06
+A07	A07
+B07	B07
+C07	C07
+D07	D07
+E07	E07
+F07	F07
+G07	G07
+H07	H07
+A08	A08
+B08	B08
+C08	C08
+D08	D08
+E08	E08
+F08	F08
+G08	G08
+H08	H08
+A09	A09
+B09	B09
+C09	C09
+D09	D09
+E09	E09
+F09	F09
+G09	G09
+H09	H09
+A10	A10
+B10	B10
+C10	C10
+D10	D10
+E10	E10
+F10	F10
+G10	G10
+H10	H10
+A11	A11
+B11	B11
+C11	C11
+D11	D11
+E11	E11
+F11	F11
+G11	G11
+H11	H11
+A12	A12
+B12	B12
+C12	C12
+D12	D12
+E12	E12
+F12	F12
+G12	G12
+H12	H12
+[DefaultLayout_DualIndex]
+A01	A01
+B01	B01
+C01	C01
+D01	D01
+E01	E01
+F01	F01
+G01	G01
+H01	H01
+A02	A02
+B02	B02
+C02	C02
+D02	D02
+E02	E02
+F02	F02
+G02	G02
+H02	H02
+A03	A03
+B03	B03
+C03	C03
+D03	D03
+E03	E03
+F03	F03
+G03	G03
+H03	H03
+A04	A04
+B04	B04
+C04	C04
+D04	D04
+E04	E04
+F04	F04
+G04	G04
+H04	H04
+A05	A05
+B05	B05
+C05	C05
+D05	D05
+E05	E05
+F05	F05
+G05	G05
+H05	H05
+A06	A06
+B06	B06
+C06	C06
+D06	D06
+E06	E06
+F06	F06
+G06	G06
+H06	H06
+A07	A07
+B07	B07
+C07	C07
+D07	D07
+E07	E07
+F07	F07
+G07	G07
+H07	H07
+A08	A08
+B08	B08
+C08	C08
+D08	D08
+E08	E08
+F08	F08
+G08	G08
+H08	H08
+A09	A09
+B09	B09
+C09	C09
+D09	D09
+E09	E09
+F09	F09
+G09	G09
+H09	H09
+A10	A10
+B10	B10
+C10	C10
+D10	D10
+E10	E10
+F10	F10
+G10	G10
+H10	H10
+A11	A11
+B11	B11
+C11	C11
+D11	D11
+E11	E11
+F11	F11
+G11	G11
+H11	H11
+A12	A12
+B12	B12
+C12	C12
+D12	D12
+E12	E12
+F12	F12
+G12	G12
+H12	H12
\ No newline at end of file
diff --git a/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set B.txt b/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set B.txt
new file mode 100644
index 00000000..ce056735
--- /dev/null
+++ b/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set B.txt	
@@ -0,0 +1,494 @@
+[Version]
+1
+[Name]
+IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set B
+[PlateExtension]
+nexud384b
+[Settings]
+Adapter	CTGTCTCTTATACACATCT
+[I7]
+UDP0097	TGCCGGTCAG
+UDP0098	CACTCAATTC
+UDP0099	TCTCACACGC
+UDP0100	TCAATGGAGA
+UDP0101	ATATGCATGT
+UDP0102	ATGGCGCCTG
+UDP0103	TCCGTTATGT
+UDP0104	GGTCTATTAA
+UDP0105	CAGCAATCGT
+UDP0106	TTCTGTAGAA
+UDP0107	GAACGCAATA
+UDP0108	AGTACTCATG
+UDP0109	GGTAGAATTA
+UDP0110	TAATTAGCGT
+UDP0111	ATTAACAAGG
+UDP0112	TGATGGCTAC
+UDP0113	GAATTACAAG
+UDP0114	TAGAATTGGA
+UDP0115	AGGCAGCTCT
+UDP0116	ATCGGCGAAG
+UDP0117	CCGTGACCGA
+UDP0118	ATACTTGTTC
+UDP0119	TCCGCCAATT
+UDP0120	AGGACAGGCC
+UDP0121	AGAGAACCTA
+UDP0122	GATATTGTGT
+UDP0123	CGTACAGGAA
+UDP0124	CTGCGTTACC
+UDP0125	AGGCCGTGGA
+UDP0126	AGGAGGTATC
+UDP0127	GCTGACGTTG
+UDP0128	CTAATAACCG
+UDP0129	TCTAGGCGCG
+UDP0130	ATAGCCAAGA
+UDP0131	TTCGGTGTGA
+UDP0132	ATGTAACGTT
+UDP0133	AACGAGGCCG
+UDP0134	TGGTGTTATG
+UDP0135	TGGCCTCTGT
+UDP0136	CCAGGCACCA
+UDP0137	CCGGTTCCTA
+UDP0138	GGCCAATATT
+UDP0139	GAATACCTAT
+UDP0140	TACGTGAAGG
+UDP0141	CTTATTGGCC
+UDP0142	ACAACTACTG
+UDP0143	GTTGGATGAA
+UDP0144	AATCCAATTG
+UDP0145	TATGATGGCC
+UDP0146	CGCAGCAATT
+UDP0147	ACGTTCCTTA
+UDP0148	CCGCGTATAG
+UDP0149	GATTCTGAAT
+UDP0150	TAGAGAATAC
+UDP0151	TTGTATCAGG
+UDP0152	CACAGCGGTC
+UDP0153	CCACGCTGAA
+UDP0154	GTTCGGAGTT
+UDP0155	ATAGCGGAAT
+UDP0156	GCAATATTCA
+UDP0157	CTAGATTGCG
+UDP0158	CGATGCGGTT
+UDP0159	TCCGGACTAG
+UDP0160	GTGACGGAGC
+UDP0161	AATTCCATCT
+UDP0162	TTAACGGTGT
+UDP0163	ACTTGTTATC
+UDP0164	CGTGTACCAG
+UDP0165	TTAACCTTCG
+UDP0166	CATATGCGAT
+UDP0167	AGCCTATGAT
+UDP0168	TATGACAATC
+UDP0169	ATGTTGTTGG
+UDP0170	GCACCACCAA
+UDP0171	AGGCGTTCGC
+UDP0172	CCTCCGGTTG
+UDP0173	GTCCACCGCT
+UDP0174	ATTGTTCGTC
+UDP0175	GGACCAGTGG
+UDP0176	CCTTCTAACA
+UDP0177	CTCGAATATA
+UDP0178	GATCGTCGCG
+UDP0179	TATCCGAGGC
+UDP0180	CGCTGTCTCA
+UDP0181	AATGCGAACA
+UDP0182	AATTCTTGGA
+UDP0183	TTCCTACAGC
+UDP0184	ATCCAGGTAT
+UDP0185	ACGGTCCAAC
+UDP0186	GTAACTTGGT
+UDP0187	AGCGCCACAC
+UDP0188	TGCTACTGCC
+UDP0189	CAACACCGCA
+UDP0190	CACCTTAATC
+UDP0191	TTGAATGTTG
+UDP0192	CCGGTAACAC
+[I5]
+UDP0097	CCTGATACAA
+UDP0098	TTAAGTTGTG
+UDP0099	CGGACAGTGA
+UDP0100	GCACTACAAC
+UDP0101	TGGTGCCTGG
+UDP0102	TCCACGGCCT
+UDP0103	TTGTAGTGTA
+UDP0104	CCACGACACG
+UDP0105	TGTGATGTAT
+UDP0106	GAGCGCAATA
+UDP0107	ATCTTACTGT
+UDP0108	ATGTCGTGGT
+UDP0109	GTAGCCATCA
+UDP0110	TGGTTAAGAA
+UDP0111	TGTTGTTCGT
+UDP0112	CCAACAACAT
+UDP0113	ACCGGCTCAG
+UDP0114	GTTAATCTGA
+UDP0115	CGGCTAACGT
+UDP0116	TCCAAGAATT
+UDP0117	CCGAACGTTG
+UDP0118	TAACCGCCGA
+UDP0119	CTCCGTGCTG
+UDP0120	CATTCCAGCT
+UDP0121	GGTTATGCTA
+UDP0122	ACCACACGGT
+UDP0123	TAGGTTCTCT
+UDP0124	TATGGCTCGA
+UDP0125	CTCGTGCGTT
+UDP0126	CCAGTTGGCA
+UDP0127	TGTTCGCATT
+UDP0128	AACCGCATCG
+UDP0129	CGAAGGTTAA
+UDP0130	AGTGCCACTG
+UDP0131	GAACAAGTAT
+UDP0132	ACGATTGCTG
+UDP0133	ATACCTGGAT
+UDP0134	TCCAATTCTA
+UDP0135	TGAGACAGCG
+UDP0136	ACGCTAATTA
+UDP0137	TATATTCGAG
+UDP0138	CGGTCCGATA
+UDP0139	ACAATAGAGT
+UDP0140	CGGTTATTAG
+UDP0141	GATAACAAGT
+UDP0142	AGTTATCACA
+UDP0143	TTCCAGGTAA
+UDP0144	CATGTAGAGG
+UDP0145	GATTGTCATA
+UDP0146	ATTCCGCTAT
+UDP0147	GACCGCTGTG
+UDP0148	TAGGAACCGG
+UDP0149	AGCGGTGGAC
+UDP0150	TATAGATTCG
+UDP0151	ACAGAGGCCA
+UDP0152	ATTCCTATTG
+UDP0153	TATTCCTCAG
+UDP0154	CGCCTTCTGA
+UDP0155	GCGCAGAGTA
+UDP0156	GGCGCCAATT
+UDP0157	AGATATGGCG
+UDP0158	CCTGCTTGGT
+UDP0159	GACGAACAAT
+UDP0160	TGGCGGTCCA
+UDP0161	CTTCAGTTAC
+UDP0162	TCCTGACCGT
+UDP0163	CGCGCCTAGA
+UDP0164	AGGATAAGTT
+UDP0165	AGGCCAGACA
+UDP0166	CCTTGAACGG
+UDP0167	CACCACCTAC
+UDP0168	TTGCTTGTAT
+UDP0169	CAATCTATGA
+UDP0170	TGGTACTGAT
+UDP0171	TTCATCCAAC
+UDP0172	CATAACACCA
+UDP0173	TCCTATTAGC
+UDP0174	TCTCTAGATT
+UDP0175	CGCGAGCCTA
+UDP0176	GATAAGCTCT
+UDP0177	GAGATGTCGA
+UDP0178	CTGGATATGT
+UDP0179	GGCCAATAAG
+UDP0180	ATTACTCACC
+UDP0181	AATTGGCGGA
+UDP0182	TTGTCAACTT
+UDP0183	GGCGAATTCT
+UDP0184	CAACGTCAGC
+UDP0185	TCTTACATCA
+UDP0186	CGCCATACCT
+UDP0187	CTAATGTCTT
+UDP0188	CAACCGGAGG
+UDP0189	GGCAGTAGCA
+UDP0190	TTAGGATAGA
+UDP0191	CGCAATCTAG
+UDP0192	GAGTTGTACT
+
+[IndexPlateLayout]
+A01	UDP0097	UDP0097
+B01	UDP0098	UDP0098
+C01	UDP0099	UDP0099
+D01	UDP0100	UDP0100
+E01	UDP0101	UDP0101
+F01	UDP0102	UDP0102
+G01	UDP0103	UDP0103
+H01	UDP0104	UDP0104
+A02	UDP0105	UDP0105
+B02	UDP0106	UDP0106
+C02	UDP0107	UDP0107
+D02	UDP0108	UDP0108
+E02	UDP0109	UDP0109
+F02	UDP0110	UDP0110
+G02	UDP0111	UDP0111
+H02	UDP0112	UDP0112
+A03	UDP0113	UDP0113
+B03	UDP0114	UDP0114
+C03	UDP0115	UDP0115
+D03	UDP0116	UDP0116
+E03	UDP0117	UDP0117
+F03	UDP0118	UDP0118
+G03	UDP0119	UDP0119
+H03	UDP0120	UDP0120
+A04	UDP0121	UDP0121
+B04	UDP0122	UDP0122
+C04	UDP0123	UDP0123
+D04	UDP0124	UDP0124
+E04	UDP0125	UDP0125
+F04	UDP0126	UDP0126
+G04	UDP0127	UDP0127
+H04	UDP0128	UDP0128
+A05	UDP0129	UDP0129
+B05	UDP0130	UDP0130
+C05	UDP0131	UDP0131
+D05	UDP0132	UDP0132
+E05	UDP0133	UDP0133
+F05	UDP0134	UDP0134
+G05	UDP0135	UDP0135
+H05	UDP0136	UDP0136
+A06	UDP0137	UDP0137
+B06	UDP0138	UDP0138
+C06	UDP0139	UDP0139
+D06	UDP0140	UDP0140
+E06	UDP0141	UDP0141
+F06	UDP0142	UDP0142
+G06	UDP0143	UDP0143
+H06	UDP0144	UDP0144
+A07	UDP0145	UDP0145
+B07	UDP0146	UDP0146
+C07	UDP0147	UDP0147
+D07	UDP0148	UDP0148
+E07	UDP0149	UDP0149
+F07	UDP0150	UDP0150
+G07	UDP0151	UDP0151
+H07	UDP0152	UDP0152
+A08	UDP0153	UDP0153
+B08	UDP0154	UDP0154
+C08	UDP0155	UDP0155
+D08	UDP0156	UDP0156
+E08	UDP0157	UDP0157
+F08	UDP0158	UDP0158
+G08	UDP0159	UDP0159
+H08	UDP0160	UDP0160
+A09	UDP0161	UDP0161
+B09	UDP0162	UDP0162
+C09	UDP0163	UDP0163
+D09	UDP0164	UDP0164
+E09	UDP0165	UDP0165
+F09	UDP0166	UDP0166
+G09	UDP0167	UDP0167
+H09	UDP0168	UDP0168
+A10	UDP0169	UDP0169
+B10	UDP0170	UDP0170
+C10	UDP0171	UDP0171
+D10	UDP0172	UDP0172
+E10	UDP0173	UDP0173
+F10	UDP0174	UDP0174
+G10	UDP0175	UDP0175
+H10	UDP0176	UDP0176
+A11	UDP0177	UDP0177
+B11	UDP0178	UDP0178
+C11	UDP0179	UDP0179
+D11	UDP0180	UDP0180
+E11	UDP0181	UDP0181
+F11	UDP0182	UDP0182
+G11	UDP0183	UDP0183
+H11	UDP0184	UDP0184
+A12	UDP0185	UDP0185
+B12	UDP0186	UDP0186
+C12	UDP0187	UDP0187
+D12	UDP0188	UDP0188
+E12	UDP0189	UDP0189
+F12	UDP0190	UDP0190
+G12	UDP0191	UDP0191
+H12	UDP0192	UDP0192
+[DefaultLayout_SingleIndex]
+A01	A01
+B01	B01
+C01	C01
+D01	D01
+E01	E01
+F01	F01
+G01	G01
+H01	H01
+A02	A02
+B02	B02
+C02	C02
+D02	D02
+E02	E02
+F02	F02
+G02	G02
+H02	H02
+A03	A03
+B03	B03
+C03	C03
+D03	D03
+E03	E03
+F03	F03
+G03	G03
+H03	H03
+A04	A04
+B04	B04
+C04	C04
+D04	D04
+E04	E04
+F04	F04
+G04	G04
+H04	H04
+A05	A05
+B05	B05
+C05	C05
+D05	D05
+E05	E05
+F05	F05
+G05	G05
+H05	H05
+A06	A06
+B06	B06
+C06	C06
+D06	D06
+E06	E06
+F06	F06
+G06	G06
+H06	H06
+A07	A07
+B07	B07
+C07	C07
+D07	D07
+E07	E07
+F07	F07
+G07	G07
+H07	H07
+A08	A08
+B08	B08
+C08	C08
+D08	D08
+E08	E08
+F08	F08
+G08	G08
+H08	H08
+A09	A09
+B09	B09
+C09	C09
+D09	D09
+E09	E09
+F09	F09
+G09	G09
+H09	H09
+A10	A10
+B10	B10
+C10	C10
+D10	D10
+E10	E10
+F10	F10
+G10	G10
+H10	H10
+A11	A11
+B11	B11
+C11	C11
+D11	D11
+E11	E11
+F11	F11
+G11	G11
+H11	H11
+A12	A12
+B12	B12
+C12	C12
+D12	D12
+E12	E12
+F12	F12
+G12	G12
+H12	H12
+[DefaultLayout_DualIndex]
+A01	A01
+B01	B01
+C01	C01
+D01	D01
+E01	E01
+F01	F01
+G01	G01
+H01	H01
+A02	A02
+B02	B02
+C02	C02
+D02	D02
+E02	E02
+F02	F02
+G02	G02
+H02	H02
+A03	A03
+B03	B03
+C03	C03
+D03	D03
+E03	E03
+F03	F03
+G03	G03
+H03	H03
+A04	A04
+B04	B04
+C04	C04
+D04	D04
+E04	E04
+F04	F04
+G04	G04
+H04	H04
+A05	A05
+B05	B05
+C05	C05
+D05	D05
+E05	E05
+F05	F05
+G05	G05
+H05	H05
+A06	A06
+B06	B06
+C06	C06
+D06	D06
+E06	E06
+F06	F06
+G06	G06
+H06	H06
+A07	A07
+B07	B07
+C07	C07
+D07	D07
+E07	E07
+F07	F07
+G07	G07
+H07	H07
+A08	A08
+B08	B08
+C08	C08
+D08	D08
+E08	E08
+F08	F08
+G08	G08
+H08	H08
+A09	A09
+B09	B09
+C09	C09
+D09	D09
+E09	E09
+F09	F09
+G09	G09
+H09	H09
+A10	A10
+B10	B10
+C10	C10
+D10	D10
+E10	E10
+F10	F10
+G10	G10
+H10	H10
+A11	A11
+B11	B11
+C11	C11
+D11	D11
+E11	E11
+F11	F11
+G11	G11
+H11	H11
+A12	A12
+B12	B12
+C12	C12
+D12	D12
+E12	E12
+F12	F12
+G12	G12
+H12	H12
\ No newline at end of file
diff --git a/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set C.txt b/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set C.txt
new file mode 100644
index 00000000..9c84b6ef
--- /dev/null
+++ b/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set C.txt	
@@ -0,0 +1,494 @@
+[Version]
+1
+[Name]
+IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set C
+[PlateExtension]
+nexud384c
+[Settings]
+Adapter	CTGTCTCTTATACACATCT
+[I7]
+UDP0193	TCTCATGATA
+UDP0194	CGAGGCCAAG
+UDP0195	TTCACGAGAC
+UDP0196	GCGTGGATGG
+UDP0197	TCCTGGTTGT
+UDP0198	TAATTCTGCT
+UDP0199	CGCACGACTG
+UDP0200	GAGGTTAGAC
+UDP0201	AACCGAGTTC
+UDP0202	TGTGATAACT
+UDP0203	AGTATGCTAC
+UDP0204	GTAACTGAAG
+UDP0205	TCCTCGGACT
+UDP0206	CTGGAACTGT
+UDP0207	GAATATGCGG
+UDP0208	GATCGGATAA
+UDP0209	GCTAGACTAT
+UDP0210	AGCTACTATA
+UDP0211	CCACCGGAGT
+UDP0212	CTTACCGCAC
+UDP0213	TTAGGATATC
+UDP0214	TTATACGCGA
+UDP0215	CGCTTAGAAT
+UDP0216	CCGAAGCGCT
+UDP0217	CACTATCAAC
+UDP0218	TTGCTCTATT
+UDP0219	TTACAGTTAG
+UDP0220	CTAAGTACGC
+UDP0221	TAGTTCGGTA
+UDP0222	CTATTACTAC
+UDP0223	TAGCATAACC
+UDP0224	ACTCTATTGT
+UDP0225	TAGTGGAAGC
+UDP0226	CGCCATATCT
+UDP0227	GCTTCATATT
+UDP0228	ACTAGCGCTA
+UDP0229	GCTCTTAACT
+UDP0230	GTGGTATCTG
+UDP0231	TGACGGCCGT
+UDP0232	CAGTAATTAC
+UDP0233	TACAAGACTT
+UDP0234	CTGTGGTGAC
+UDP0235	CTCCACTAAT
+UDP0236	ATAGTTAGCA
+UDP0237	ATAGGTCTTA
+UDP0238	TTCTTAACCA
+UDP0239	AAGGAAGAGT
+UDP0240	GGAAGGAGAC
+UDP0241	TGAACGCGGA
+UDP0242	CCTGCAACCT
+UDP0243	TTCATGGTTC
+UDP0244	ATCCTCTCAA
+UDP0245	CACTAGACCA
+UDP0246	ATTATCCACT
+UDP0247	ATGGCGTGCC
+UDP0248	TCCAGAGATC
+UDP0249	ATGTCCAGCA
+UDP0250	CAACGTTCGG
+UDP0251	GCGTATTAAT
+UDP0252	GTTGTGACTA
+UDP0253	TCTCAATACC
+UDP0254	AAGCATCTTG
+UDP0255	TCAGTCTCGT
+UDP0256	TGCAAGATAA
+UDP0257	GTAACAATCT
+UDP0258	CAGCGGTAGA
+UDP0259	TCATACCGTT
+UDP0260	GGCGCCATTG
+UDP0261	AGCGAATTAG
+UDP0262	TTAGACCATG
+UDP0263	CACACAGTAT
+UDP0264	TCTTGTCGGC
+UDP0265	TACCGCCTCG
+UDP0266	CTGTTATATC
+UDP0267	TAACCGGCGA
+UDP0268	AAGAGAGTCT
+UDP0269	GTAGGCGAGC
+UDP0270	AACTTATCCT
+UDP0271	ATTATGTCTC
+UDP0272	TATAACAGCT
+UDP0273	CCAATGATAC
+UDP0274	GAGGCCTATT
+UDP0275	AGCTAAGCGG
+UDP0276	CTTCCTAGGA
+UDP0277	CGATCTGTGA
+UDP0278	GTGGACAAGT
+UDP0279	AACAAGTACA
+UDP0280	AGATTAAGTG
+UDP0281	TATCACTCTG
+UDP0282	AGAATTCGCC
+UDP0283	CCTGACCACT
+UDP0284	AGCTGGAATG
+UDP0285	TGATAACGAG
+UDP0286	CATAGTAAGG
+UDP0287	ATTGGCTTCT
+UDP0288	GTACCGATTA
+[I5]
+UDP0193	AACACGTGGA
+UDP0194	GTGTTACCGG
+UDP0195	AGATTGTTAC
+UDP0196	TTGACCAATG
+UDP0197	CTGACCGGCA
+UDP0198	TCTCATCAAT
+UDP0199	GGACCAACAG
+UDP0200	AATGTATTGC
+UDP0201	GATCTCTGGA
+UDP0202	CAGGCGCCAT
+UDP0203	TTAATAGACC
+UDP0204	GGAGTCGCGA
+UDP0205	AACGCCAGAG
+UDP0206	CGTAATTAAC
+UDP0207	ACGAGACTGA
+UDP0208	GTATCGGCCG
+UDP0209	AATACGACAT
+UDP0210	GTTATATGGC
+UDP0211	GCCTGCCATG
+UDP0212	TAAGACCTAT
+UDP0213	TATACCATGG
+UDP0214	GCCGTCTGTT
+UDP0215	CAGAGTGATA
+UDP0216	TGCTAACTAT
+UDP0217	TCAGTTAATG
+UDP0218	GTGACCTTGA
+UDP0219	ACATGCATAT
+UDP0220	AACATACCTA
+UDP0221	CCATGTGTAG
+UDP0222	GAGTCTCTCC
+UDP0223	GCTATGCGCA
+UDP0224	ATCGCATATG
+UDP0225	AGTACCTATA
+UDP0226	GACCGGAGAT
+UDP0227	CGTTCAGCCT
+UDP0228	TTACTTCCTC
+UDP0229	CACGTCCACC
+UDP0230	GCTACTATCT
+UDP0231	AGTCAACCAT
+UDP0232	CGAGGCGGTA
+UDP0233	CAGGTGTTCA
+UDP0234	GACAGACAGG
+UDP0235	TGTACTTGTT
+UDP0236	CTCTAAGTAG
+UDP0237	GTCACCACAG
+UDP0238	TCTACATACC
+UDP0239	CACGTTAGGC
+UDP0240	TGGTGAGTCT
+UDP0241	CTTCGAAGGA
+UDP0242	GTAGAGTCAG
+UDP0243	GACATTGTCA
+UDP0244	TCCGCAAGGC
+UDP0245	ACTGCCTTAT
+UDP0246	TACGCACGTA
+UDP0247	CGCTTGAAGT
+UDP0248	CTGCACTTCA
+UDP0249	CAGCGGACAA
+UDP0250	GGATCCGCAT
+UDP0251	TGCGGTGTTG
+UDP0252	ACATAACGGA
+UDP0253	GACGTTCGCG
+UDP0254	CATTCAACAA
+UDP0255	CACGGATTAT
+UDP0256	TTGAGGACGG
+UDP0257	CTCTGTATAC
+UDP0258	GCAACAGGTG
+UDP0259	GGTAACGCAG
+UDP0260	ACCGCGCAAT
+UDP0261	AGCCGGAACA
+UDP0262	TCCTAGGAAG
+UDP0263	TTGAGCCTAA
+UDP0264	CCACCTGTGT
+UDP0265	CCTCGCAACC
+UDP0266	GTATAGCTGT
+UDP0267	GCTACATTAG
+UDP0268	TACGAATCTT
+UDP0269	TAGGAGCGCA
+UDP0270	GTACTGGCGT
+UDP0271	AGTTAAGAGC
+UDP0272	TCGCGTATAA
+UDP0273	GAGTGTGCCG
+UDP0274	CTAGTCCGGA
+UDP0275	ATTAATACGC
+UDP0276	CCTAGAGTAT
+UDP0277	TAGGAAGACT
+UDP0278	CCGTGGCCTT
+UDP0279	GGATATATCC
+UDP0280	CACCTCTTGG
+UDP0281	AACGTTACAT
+UDP0282	CGGCAAGCTC
+UDP0283	TCTTGGCTAT
+UDP0284	ACGGAATGCG
+UDP0285	GTTCCGCAGG
+UDP0286	ACCAAGTTAC
+UDP0287	TGGCTCGCAG
+UDP0288	AACTAACGTT
+
+[IndexPlateLayout]
+A01	UDP0193	UDP0193
+B01	UDP0194	UDP0194
+C01	UDP0195	UDP0195
+D01	UDP0196	UDP0196
+E01	UDP0197	UDP0197
+F01	UDP0198	UDP0198
+G01	UDP0199	UDP0199
+H01	UDP0200	UDP0200
+A02	UDP0201	UDP0201
+B02	UDP0202	UDP0202
+C02	UDP0203	UDP0203
+D02	UDP0204	UDP0204
+E02	UDP0205	UDP0205
+F02	UDP0206	UDP0206
+G02	UDP0207	UDP0207
+H02	UDP0208	UDP0208
+A03	UDP0209	UDP0209
+B03	UDP0210	UDP0210
+C03	UDP0211	UDP0211
+D03	UDP0212	UDP0212
+E03	UDP0213	UDP0213
+F03	UDP0214	UDP0214
+G03	UDP0215	UDP0215
+H03	UDP0216	UDP0216
+A04	UDP0217	UDP0217
+B04	UDP0218	UDP0218
+C04	UDP0219	UDP0219
+D04	UDP0220	UDP0220
+E04	UDP0221	UDP0221
+F04	UDP0222	UDP0222
+G04	UDP0223	UDP0223
+H04	UDP0224	UDP0224
+A05	UDP0225	UDP0225
+B05	UDP0226	UDP0226
+C05	UDP0227	UDP0227
+D05	UDP0228	UDP0228
+E05	UDP0229	UDP0229
+F05	UDP0230	UDP0230
+G05	UDP0231	UDP0231
+H05	UDP0232	UDP0232
+A06	UDP0233	UDP0233
+B06	UDP0234	UDP0234
+C06	UDP0235	UDP0235
+D06	UDP0236	UDP0236
+E06	UDP0237	UDP0237
+F06	UDP0238	UDP0238
+G06	UDP0239	UDP0239
+H06	UDP0240	UDP0240
+A07	UDP0241	UDP0241
+B07	UDP0242	UDP0242
+C07	UDP0243	UDP0243
+D07	UDP0244	UDP0244
+E07	UDP0245	UDP0245
+F07	UDP0246	UDP0246
+G07	UDP0247	UDP0247
+H07	UDP0248	UDP0248
+A08	UDP0249	UDP0249
+B08	UDP0250	UDP0250
+C08	UDP0251	UDP0251
+D08	UDP0252	UDP0252
+E08	UDP0253	UDP0253
+F08	UDP0254	UDP0254
+G08	UDP0255	UDP0255
+H08	UDP0256	UDP0256
+A09	UDP0257	UDP0257
+B09	UDP0258	UDP0258
+C09	UDP0259	UDP0259
+D09	UDP0260	UDP0260
+E09	UDP0261	UDP0261
+F09	UDP0262	UDP0262
+G09	UDP0263	UDP0263
+H09	UDP0264	UDP0264
+A10	UDP0265	UDP0265
+B10	UDP0266	UDP0266
+C10	UDP0267	UDP0267
+D10	UDP0268	UDP0268
+E10	UDP0269	UDP0269
+F10	UDP0270	UDP0270
+G10	UDP0271	UDP0271
+H10	UDP0272	UDP0272
+A11	UDP0273	UDP0273
+B11	UDP0274	UDP0274
+C11	UDP0275	UDP0275
+D11	UDP0276	UDP0276
+E11	UDP0277	UDP0277
+F11	UDP0278	UDP0278
+G11	UDP0279	UDP0279
+H11	UDP0280	UDP0280
+A12	UDP0281	UDP0281
+B12	UDP0282	UDP0282
+C12	UDP0283	UDP0283
+D12	UDP0284	UDP0284
+E12	UDP0285	UDP0285
+F12	UDP0286	UDP0286
+G12	UDP0287	UDP0287
+H12	UDP0288	UDP0288
+[DefaultLayout_SingleIndex]
+A01	A01
+B01	B01
+C01	C01
+D01	D01
+E01	E01
+F01	F01
+G01	G01
+H01	H01
+A02	A02
+B02	B02
+C02	C02
+D02	D02
+E02	E02
+F02	F02
+G02	G02
+H02	H02
+A03	A03
+B03	B03
+C03	C03
+D03	D03
+E03	E03
+F03	F03
+G03	G03
+H03	H03
+A04	A04
+B04	B04
+C04	C04
+D04	D04
+E04	E04
+F04	F04
+G04	G04
+H04	H04
+A05	A05
+B05	B05
+C05	C05
+D05	D05
+E05	E05
+F05	F05
+G05	G05
+H05	H05
+A06	A06
+B06	B06
+C06	C06
+D06	D06
+E06	E06
+F06	F06
+G06	G06
+H06	H06
+A07	A07
+B07	B07
+C07	C07
+D07	D07
+E07	E07
+F07	F07
+G07	G07
+H07	H07
+A08	A08
+B08	B08
+C08	C08
+D08	D08
+E08	E08
+F08	F08
+G08	G08
+H08	H08
+A09	A09
+B09	B09
+C09	C09
+D09	D09
+E09	E09
+F09	F09
+G09	G09
+H09	H09
+A10	A10
+B10	B10
+C10	C10
+D10	D10
+E10	E10
+F10	F10
+G10	G10
+H10	H10
+A11	A11
+B11	B11
+C11	C11
+D11	D11
+E11	E11
+F11	F11
+G11	G11
+H11	H11
+A12	A12
+B12	B12
+C12	C12
+D12	D12
+E12	E12
+F12	F12
+G12	G12
+H12	H12
+[DefaultLayout_DualIndex]
+A01	A01
+B01	B01
+C01	C01
+D01	D01
+E01	E01
+F01	F01
+G01	G01
+H01	H01
+A02	A02
+B02	B02
+C02	C02
+D02	D02
+E02	E02
+F02	F02
+G02	G02
+H02	H02
+A03	A03
+B03	B03
+C03	C03
+D03	D03
+E03	E03
+F03	F03
+G03	G03
+H03	H03
+A04	A04
+B04	B04
+C04	C04
+D04	D04
+E04	E04
+F04	F04
+G04	G04
+H04	H04
+A05	A05
+B05	B05
+C05	C05
+D05	D05
+E05	E05
+F05	F05
+G05	G05
+H05	H05
+A06	A06
+B06	B06
+C06	C06
+D06	D06
+E06	E06
+F06	F06
+G06	G06
+H06	H06
+A07	A07
+B07	B07
+C07	C07
+D07	D07
+E07	E07
+F07	F07
+G07	G07
+H07	H07
+A08	A08
+B08	B08
+C08	C08
+D08	D08
+E08	E08
+F08	F08
+G08	G08
+H08	H08
+A09	A09
+B09	B09
+C09	C09
+D09	D09
+E09	E09
+F09	F09
+G09	G09
+H09	H09
+A10	A10
+B10	B10
+C10	C10
+D10	D10
+E10	E10
+F10	F10
+G10	G10
+H10	H10
+A11	A11
+B11	B11
+C11	C11
+D11	D11
+E11	E11
+F11	F11
+G11	G11
+H11	H11
+A12	A12
+B12	B12
+C12	C12
+D12	D12
+E12	E12
+F12	F12
+G12	G12
+H12	H12
\ No newline at end of file
diff --git a/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set D.txt b/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set D.txt
new file mode 100644
index 00000000..ae4f63a7
--- /dev/null
+++ b/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set D.txt	
@@ -0,0 +1,497 @@
+[Version]
+1
+[Name]
+IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set D
+[PlateExtension]
+nexud384d
+[Settings]
+Adapter	CTGTCTCTTATACACATCT
+[I7]
+UDP0289	GAACAATTCC
+UDP0290	TGTGGTCCGG
+UDP0291	CTTCTAAGTC
+UDP0292	AATATTGCCA
+UDP0293	TCGTGCATTC
+UDP0294	AAGATACACG
+UDP0295	TGCAATGAAT
+UDP0296	CTATGAAGGA
+UDP0297	GAAGACTAGA
+UDP0298	AGGAGTCGAG
+UDP0299	TTCACTCACT
+UDP0300	GGTCCGCTTC
+UDP0301	CAACGAGAGC
+UDP0302	ATTGAGGTCC
+UDP0303	GGAGAGACTC
+UDP0304	CCGCTCCGTT
+UDP0305	ATACATCACA
+UDP0306	TAGGTATGTT
+UDP0307	CACCTAGCAC
+UDP0308	TTCAAGTATG
+UDP0309	TTAAGACAAG
+UDP0310	CACCTCTCTT
+UDP0311	TTCTCGTGCA
+UDP0312	GCTAGGAAGT
+UDP0313	TTAATAGCAC
+UDP0314	CATTCACGCT
+UDP0315	GGCACTAAGG
+UDP0316	ATTCGGTACA
+UDP0317	ACTAATCTCC
+UDP0318	TGTGTTAGTA
+UDP0319	CAACGACCTA
+UDP0320	CGGTCGGCAT
+UDP0321	TCGACGCTAG
+UDP0322	CTCGTAGGCA
+UDP0323	AAGTTCTAGT
+UDP0324	CCAAGAGGTG
+UDP0325	ATATCTGCTT
+UDP0326	TGGATCTGGC
+UDP0327	TTGAATCCAA
+UDP0328	CACGGCTAGT
+UDP0329	GAGCTTGCCG
+UDP0330	AGCTAGCTTC
+UDP0331	CAATCCTTGT
+UDP0332	CACCTGTTGC
+UDP0333	CGTCACCTTG
+UDP0334	AATGACTGGT
+UDP0335	ATGATTCCGG
+UDP0336	TTAGGCTCAA
+UDP0337	TGTAAGGTGG
+UDP0338	CAACTGCAAC
+UDP0339	ACATGAGTGA
+UDP0340	GCAACCAGTC
+UDP0341	GAGCGACGAT
+UDP0342	CGAACGCACC
+UDP0343	TCTTACGCCG
+UDP0344	AGCTGATGTC
+UDP0345	CTGAATTAGT
+UDP0346	TAAGGAGGAA
+UDP0347	AGCTTACACA
+UDP0348	AACCAGCCAC
+UDP0349	CTTAAGTCGA
+UDP0350	GCCTAACGTG
+UDP0351	ACTTACTTCA
+UDP0352	CGCATTCCGT
+UDP0353	GATATCACAC
+UDP0354	AGCGCTGTGT
+UDP0355	TCACCGCGCT
+UDP0356	GATAGCCTTG
+UDP0357	CCTGGACGCA
+UDP0358	TTACGCACCT
+UDP0359	TCGTTGCTGC
+UDP0360	CGACAAGGAT
+UDP0361	GTGTACCTTC
+UDP0362	ACCTGGCCAA
+UDP0363	TGTCTGGCCT
+UDP0364	AGTTAATGCT
+UDP0365	GGTGAGTAAT
+UDP0366	TACTCTGCGC
+UDP0367	AGGTATGGCG
+UDP0368	TCCAGCCTGC
+UDP0369	GCCATATAAC
+UDP0370	AGTGCGAGTG
+UDP0371	CTGAGCCGGT
+UDP0372	AACGGTCTAT
+UDP0373	GTTGCGTTCA
+UDP0374	CTTCAACCAC
+UDP0375	TCTATTCAGT
+UDP0376	CAAGACGTCC
+UDP0377	TGAGTACAAC
+UDP0378	CCGCGGTTCT
+UDP0379	ATTGATACTG
+UDP0380	GGATTATGGA
+UDP0381	TGGTTCTCAT
+UDP0382	TCAACCACGA
+UDP0383	TATGAACTTG
+UDP0384	AGTGGTTAAG
+
+[I5]
+UDP0289	TAGAGTTGGA
+UDP0290	AGAGCACTAG
+UDP0291	ACTCTACAGG
+UDP0292	CGGTGACACC
+UDP0293	GCGTTGGTAT
+UDP0294	TGTGCTAACA
+UDP0295	CCAGAAGTAA
+UDP0296	CTTATACCTG
+UDP0297	ACTAGAACTT
+UDP0298	TTAGGCTTAC
+UDP0299	TATCATGAGA
+UDP0300	CTCACACAAG
+UDP0301	GAATTGAGTG
+UDP0302	CGGATTATAT
+UDP0303	TTGAAGCAGA
+UDP0304	TACGGCGAAG
+UDP0305	TCTCCATTGA
+UDP0306	CGAGACCAAG
+UDP0307	TGCTGGACAT
+UDP0308	GATGGTATCG
+UDP0309	GGCTTAATTG
+UDP0310	CTCGACTCCT
+UDP0311	ATACACAGAG
+UDP0312	TCTCGGACGA
+UDP0313	ACCACGTCTG
+UDP0314	GTTGTACTCA
+UDP0315	TCAGGTCAAC
+UDP0316	AGTCCGAGGA
+UDP0317	CACTTAATCT
+UDP0318	TACTCTGTTA
+UDP0319	GCGACTCGAT
+UDP0320	CTAGGCAAGG
+UDP0321	CCTCTTCGAA
+UDP0322	TCATCCTCTT
+UDP0323	GGTAAGATAA
+UDP0324	AACGAGCCAG
+UDP0325	TAGACAATCT
+UDP0326	CAATGCTGAA
+UDP0327	GTCACGGTGT
+UDP0328	GGTGTACAAG
+UDP0329	AGGTTGCAGG
+UDP0330	TAATACGGAG
+UDP0331	CGAAGACGCA
+UDP0332	ATTGACACAT
+UDP0333	CAGCCGATTG
+UDP0334	TCTCACGCGT
+UDP0335	CTCTGACGTG
+UDP0336	TCGAATGGAA
+UDP0337	AAGGCCTTGG
+UDP0338	TGAACGCAAC
+UDP0339	CCGCTTAGCT
+UDP0340	CACCGAGGAA
+UDP0341	CGTATAATCA
+UDP0342	ATGACAGAAC
+UDP0343	ATTCATTGCA
+UDP0344	TCATGTCCTG
+UDP0345	AATTCGATCG
+UDP0346	TTCCGACATT
+UDP0347	TGGCACGACC
+UDP0348	GCCACAGCAC
+UDP0349	CAGTAGTTGT
+UDP0350	AGCTCTCAAG
+UDP0351	TCTGGAATTA
+UDP0352	ATTAGTGGAG
+UDP0353	GACTATATGT
+UDP0354	CGTTCGGAAC
+UDP0355	TCGATACTAG
+UDP0356	TACCACAATG
+UDP0357	TGGTATACCA
+UDP0358	GCTCTCGTTG
+UDP0359	GTCTCGTGAA
+UDP0360	AAGGCCACCT
+UDP0361	CTGTGAGCTA
+UDP0362	TCACAGATCG
+UDP0363	AGAAGCCAAT
+UDP0364	ACTGCAGCCG
+UDP0365	AACATCTAGT
+UDP0366	CCTTACTATG
+UDP0367	GTGGCGAGAC
+UDP0368	GCCAGATCCA
+UDP0369	ACACAATATC
+UDP0370	TGGAGGTAAT
+UDP0371	CCTTCACGTA
+UDP0372	CTATACGCGG
+UDP0373	GTTGCAGTTG
+UDP0374	TTATGCGCCT
+UDP0375	TCTCAGTACA
+UDP0376	AGTATACGGA
+UDP0377	ACGCTTGGAC
+UDP0378	GGAGTAGATT
+UDP0379	TACACGCTCC
+UDP0380	TCCGATAGAG
+UDP0381	CTCAAGGCCG
+UDP0382	CAAGTTCATA
+UDP0383	AATCCTTAGG
+UDP0384	GGTGGAATAC
+
+
+[IndexPlateLayout]
+A01	UDP0289	UDP0289
+B01	UDP0290	UDP0290
+C01	UDP0291	UDP0291
+D01	UDP0292	UDP0292
+E01	UDP0293	UDP0293
+F01	UDP0294	UDP0294
+G01	UDP0295	UDP0295
+H01	UDP0296	UDP0296
+A02	UDP0297	UDP0297
+B02	UDP0298	UDP0298
+C02	UDP0299	UDP0299
+D02	UDP0300	UDP0300
+E02	UDP0301	UDP0301
+F02	UDP0302	UDP0302
+G02	UDP0303	UDP0303
+H02	UDP0304	UDP0304
+A03	UDP0305	UDP0305
+B03	UDP0306	UDP0306
+C03	UDP0307	UDP0307
+D03	UDP0308	UDP0308
+E03	UDP0309	UDP0309
+F03	UDP0310	UDP0310
+G03	UDP0311	UDP0311
+H03	UDP0312	UDP0312
+A04	UDP0313	UDP0313
+B04	UDP0314	UDP0314
+C04	UDP0315	UDP0315
+D04	UDP0316	UDP0316
+E04	UDP0317	UDP0317
+F04	UDP0318	UDP0318
+G04	UDP0319	UDP0319
+H04	UDP0320	UDP0320
+A05	UDP0321	UDP0321
+B05	UDP0322	UDP0322
+C05	UDP0323	UDP0323
+D05	UDP0324	UDP0324
+E05	UDP0325	UDP0325
+F05	UDP0326	UDP0326
+G05	UDP0327	UDP0327
+H05	UDP0328	UDP0328
+A06	UDP0329	UDP0329
+B06	UDP0330	UDP0330
+C06	UDP0331	UDP0331
+D06	UDP0332	UDP0332
+E06	UDP0333	UDP0333
+F06	UDP0334	UDP0334
+G06	UDP0335	UDP0335
+H06	UDP0336	UDP0336
+A07	UDP0337	UDP0337
+B07	UDP0338	UDP0338
+C07	UDP0339	UDP0339
+D07	UDP0340	UDP0340
+E07	UDP0341	UDP0341
+F07	UDP0342	UDP0342
+G07	UDP0343	UDP0343
+H07	UDP0344	UDP0344
+A08	UDP0345	UDP0345
+B08	UDP0346	UDP0346
+C08	UDP0347	UDP0347
+D08	UDP0348	UDP0348
+E08	UDP0349	UDP0349
+F08	UDP0350	UDP0350
+G08	UDP0351	UDP0351
+H08	UDP0352	UDP0352
+A09	UDP0353	UDP0353
+B09	UDP0354	UDP0354
+C09	UDP0355	UDP0355
+D09	UDP0356	UDP0356
+E09	UDP0357	UDP0357
+F09	UDP0358	UDP0358
+G09	UDP0359	UDP0359
+H09	UDP0360	UDP0360
+A10	UDP0361	UDP0361
+B10	UDP0362	UDP0362
+C10	UDP0363	UDP0363
+D10	UDP0364	UDP0364
+E10	UDP0365	UDP0365
+F10	UDP0366	UDP0366
+G10	UDP0367	UDP0367
+H10	UDP0368	UDP0368
+A11	UDP0369	UDP0369
+B11	UDP0370	UDP0370
+C11	UDP0371	UDP0371
+D11	UDP0372	UDP0372
+E11	UDP0373	UDP0373
+F11	UDP0374	UDP0374
+G11	UDP0375	UDP0375
+H11	UDP0376	UDP0376
+A12	UDP0377	UDP0377
+B12	UDP0378	UDP0378
+C12	UDP0379	UDP0379
+D12	UDP0380	UDP0380
+E12	UDP0381	UDP0381
+F12	UDP0382	UDP0382
+G12	UDP0383	UDP0383
+H12	UDP0384	UDP0384
+
+[DefaultLayout_SingleIndex]
+A01	A01
+B01	B01
+C01	C01
+D01	D01
+E01	E01
+F01	F01
+G01	G01
+H01	H01
+A02	A02
+B02	B02
+C02	C02
+D02	D02
+E02	E02
+F02	F02
+G02	G02
+H02	H02
+A03	A03
+B03	B03
+C03	C03
+D03	D03
+E03	E03
+F03	F03
+G03	G03
+H03	H03
+A04	A04
+B04	B04
+C04	C04
+D04	D04
+E04	E04
+F04	F04
+G04	G04
+H04	H04
+A05	A05
+B05	B05
+C05	C05
+D05	D05
+E05	E05
+F05	F05
+G05	G05
+H05	H05
+A06	A06
+B06	B06
+C06	C06
+D06	D06
+E06	E06
+F06	F06
+G06	G06
+H06	H06
+A07	A07
+B07	B07
+C07	C07
+D07	D07
+E07	E07
+F07	F07
+G07	G07
+H07	H07
+A08	A08
+B08	B08
+C08	C08
+D08	D08
+E08	E08
+F08	F08
+G08	G08
+H08	H08
+A09	A09
+B09	B09
+C09	C09
+D09	D09
+E09	E09
+F09	F09
+G09	G09
+H09	H09
+A10	A10
+B10	B10
+C10	C10
+D10	D10
+E10	E10
+F10	F10
+G10	G10
+H10	H10
+A11	A11
+B11	B11
+C11	C11
+D11	D11
+E11	E11
+F11	F11
+G11	G11
+H11	H11
+A12	A12
+B12	B12
+C12	C12
+D12	D12
+E12	E12
+F12	F12
+G12	G12
+H12	H12
+[DefaultLayout_DualIndex]
+A01	A01
+B01	B01
+C01	C01
+D01	D01
+E01	E01
+F01	F01
+G01	G01
+H01	H01
+A02	A02
+B02	B02
+C02	C02
+D02	D02
+E02	E02
+F02	F02
+G02	G02
+H02	H02
+A03	A03
+B03	B03
+C03	C03
+D03	D03
+E03	E03
+F03	F03
+G03	G03
+H03	H03
+A04	A04
+B04	B04
+C04	C04
+D04	D04
+E04	E04
+F04	F04
+G04	G04
+H04	H04
+A05	A05
+B05	B05
+C05	C05
+D05	D05
+E05	E05
+F05	F05
+G05	G05
+H05	H05
+A06	A06
+B06	B06
+C06	C06
+D06	D06
+E06	E06
+F06	F06
+G06	G06
+H06	H06
+A07	A07
+B07	B07
+C07	C07
+D07	D07
+E07	E07
+F07	F07
+G07	G07
+H07	H07
+A08	A08
+B08	B08
+C08	C08
+D08	D08
+E08	E08
+F08	F08
+G08	G08
+H08	H08
+A09	A09
+B09	B09
+C09	C09
+D09	D09
+E09	E09
+F09	F09
+G09	G09
+H09	H09
+A10	A10
+B10	B10
+C10	C10
+D10	D10
+E10	E10
+F10	F10
+G10	G10
+H10	H10
+A11	A11
+B11	B11
+C11	C11
+D11	D11
+E11	E11
+F11	F11
+G11	G11
+H11	H11
+A12	A12
+B12	B12
+C12	C12
+D12	D12
+E12	E12
+F12	F12
+G12	G12
+H12	H12
\ No newline at end of file
diff --git a/conf/collection_index_klits/Nextera DNA CD Indexes (96 indexes plated).txt b/conf/collection_index_klits/Nextera DNA CD Indexes (96 indexes plated).txt
new file mode 100644
index 00000000..6b990e85
--- /dev/null
+++ b/conf/collection_index_klits/Nextera DNA CD Indexes (96 indexes plated).txt	
@@ -0,0 +1,321 @@
+[Version]
+1
+[Name]
+Nextera DNA CD Indexes (96 Indexes plated)
+[PlateExtension]
+nex96
+[Settings]
+Adapter	CTGTCTCTTATACACATCT
+[I7]
+H701	TAAGGCGA
+H702	CGTACTAG
+H703	AGGCAGAA
+H705	GGACTCCT
+H706	TAGGCATG
+H707	CTCTCTAC
+H710	CGAGGCTG
+H711	AAGAGGCA
+H712	GTAGAGGA
+H714	GCTCATGA
+H720	CGGAGCCT
+H723	TAGCGCTC
+[I5]
+H503	TATCCTCT
+H505	GTAAGGAG
+H506	ACTGCATA
+H510	CGTCTAAT
+H513	TCGACTAG
+H516	CCTAGAGT
+H517	GCGTAAGA
+H522	TTATGCGA
+[IndexPlateLayout]
+A01	H701	H505
+A02	H702	H506
+A03	H703	H517
+A04	H705	H505
+A05	H707	H506
+A06	H723	H517
+A07	H706	H505
+A08	H712	H506
+A09	H720	H517
+A10	H710	H505
+A11	H711	H506
+A12	H714	H517
+B01	H702	H517
+B02	H703	H505
+B03	H701	H506
+B04	H707	H517
+B05	H723	H505
+B06	H705	H506
+B07	H712	H517
+B08	H720	H505
+B09	H706	H506
+B10	H711	H517
+B11	H714	H505
+B12	H710	H506
+C01	H703	H506
+C02	H701	H517
+C03	H702	H505
+C04	H723	H506
+C05	H705	H517
+C06	H707	H505
+C07	H720	H506
+C08	H706	H517
+C09	H712	H505
+C10	H714	H506
+C11	H710	H517
+C12	H711	H505
+D01	H705	H503
+D02	H707	H503
+D03	H723	H503
+D04	H706	H503
+D05	H712	H503
+D06	H720	H503
+D07	H710	H503
+D08	H711	H503
+D09	H714	H503
+D10	H701	H503
+D11	H702	H503
+D12	H703	H503
+E01	H706	H516
+E02	H712	H516
+E03	H720	H516
+E04	H710	H516
+E05	H711	H516
+E06	H714	H516
+E07	H701	H516
+E08	H702	H516
+E09	H703	H516
+E10	H705	H516
+E11	H707	H516
+E12	H723	H516
+F01	H710	H522
+F02	H711	H510
+F03	H714	H513
+F04	H701	H522
+F05	H702	H510
+F06	H703	H513
+F07	H705	H522
+F08	H707	H510
+F09	H723	H513
+F10	H706	H522
+F11	H712	H510
+F12	H720	H513
+G01	H711	H513
+G02	H714	H522
+G03	H710	H510
+G04	H702	H513
+G05	H703	H522
+G06	H701	H510
+G07	H707	H513
+G08	H723	H522
+G09	H705	H510
+G10	H712	H513
+G11	H720	H522
+G12	H706	H510
+H01	H714	H510
+H02	H710	H513
+H03	H711	H522
+H04	H703	H510
+H05	H701	H513
+H06	H702	H522
+H07	H723	H510
+H08	H705	H513
+H09	H707	H522
+H10	H720	H510
+H11	H706	H513
+H12	H712	H522
+[DefaultLayout_SingleIndex]
+A01	A01
+B01	B01
+C01	C01
+D01	D01
+E01	E01
+F01	F01
+G01	G01
+H01	H01
+A02	A02
+B02	B02
+C02	C02
+D02	D02
+E02	E02
+F02	F02
+G02	G02
+H02	H02
+A03	A03
+B03	B03
+C03	C03
+D03	D03
+E03	E03
+F03	F03
+G03	G03
+H03	H03
+A04	A04
+B04	B04
+C04	C04
+D04	D04
+E04	E04
+F04	F04
+G04	G04
+H04	H04
+A05	A05
+B05	B05
+C05	C05
+D05	D05
+E05	E05
+F05	F05
+G05	G05
+H05	H05
+A06	A06
+B06	B06
+C06	C06
+D06	D06
+E06	E06
+F06	F06
+G06	G06
+H06	H06
+A07	A07
+B07	B07
+C07	C07
+D07	D07
+E07	E07
+F07	F07
+G07	G07
+H07	H07
+A08	A08
+B08	B08
+C08	C08
+D08	D08
+E08	E08
+F08	F08
+G08	G08
+H08	H08
+A09	A09
+B09	B09
+C09	C09
+D09	D09
+E09	E09
+F09	F09
+G09	G09
+H09	H09
+A10	A10
+B10	B10
+C10	C10
+D10	D10
+E10	E10
+F10	F10
+G10	G10
+H10	H10
+A11	A11
+B11	B11
+C11	C11
+D11	D11
+E11	E11
+F11	F11
+G11	G11
+H11	H11
+A12	A12
+B12	B12
+C12	C12
+D12	D12
+E12	E12
+F12	F12
+G12	G12
+H12	H12
+[DefaultLayout_DualIndex]
+A01	A01
+B01	B01
+C01	C01
+D01	D01
+E01	E01
+F01	F01
+G01	G01
+H01	H01
+A02	A02
+B02	B02
+C02	C02
+D02	D02
+E02	E02
+F02	F02
+G02	G02
+H02	H02
+A03	A03
+B03	B03
+C03	C03
+D03	D03
+E03	E03
+F03	F03
+G03	G03
+H03	H03
+A04	A04
+B04	B04
+C04	C04
+D04	D04
+E04	E04
+F04	F04
+G04	G04
+H04	H04
+A05	A05
+B05	B05
+C05	C05
+D05	D05
+E05	E05
+F05	F05
+G05	G05
+H05	H05
+A06	A06
+B06	B06
+C06	C06
+D06	D06
+E06	E06
+F06	F06
+G06	G06
+H06	H06
+A07	A07
+B07	B07
+C07	C07
+D07	D07
+E07	E07
+F07	F07
+G07	G07
+H07	H07
+A08	A08
+B08	B08
+C08	C08
+D08	D08
+E08	E08
+F08	F08
+G08	G08
+H08	H08
+A09	A09
+B09	B09
+C09	C09
+D09	D09
+E09	E09
+F09	F09
+G09	G09
+H09	H09
+A10	A10
+B10	B10
+C10	C10
+D10	D10
+E10	E10
+F10	F10
+G10	G10
+H10	H10
+A11	A11
+B11	B11
+C11	C11
+D11	D11
+E11	E11
+F11	F11
+G11	G11
+H11	H11
+A12	A12
+B12	B12
+C12	C12
+D12	D12
+E12	E12
+F12	F12
+G12	G12
+H12	H12
\ No newline at end of file
diff --git a/conf/collection_index_klits/Nextera Index Kit (24 Indexes 96 Samples).txt b/conf/collection_index_klits/Nextera Index Kit (24 Indexes 96 Samples).txt
new file mode 100644
index 00000000..168e6960
--- /dev/null
+++ b/conf/collection_index_klits/Nextera Index Kit (24 Indexes 96 Samples).txt	
@@ -0,0 +1,70 @@
+[Version]
+1
+[Name]
+Nextera Index Kit (24 Indexes 96 Samples)
+[PlateExtension]
+nexfc36
+[Settings]
+Adapter	CTGTCTCTTATACACATCT
+[I7]
+N701	TAAGGCGA
+N702	CGTACTAG
+N703	AGGCAGAA
+N704	TCCTGAGC
+N705	GGACTCCT
+N706	TAGGCATG
+[I5]
+N502	CTCTCTAT
+N503	TATCCTCT
+N504	AGAGTAGA
+N517	GCGTAAGA
+[DefaultLayout_SingleIndex]
+A01	N701
+B01	N701
+C01	N701
+D01	N701
+A02	N702
+B02	N702
+C02	N702
+D02	N702
+A03	N703
+B03	N703
+C03	N703
+D03	N703
+A04	N704
+B04	N704
+C04	N704
+D04	N704
+A05	N705
+B05	N705
+C05	N705
+D05	N705
+A06	N706
+B06	N706
+C06	N706
+D06	N706	
+[DefaultLayout_DualIndex]
+A01	N701	N502
+B01	N701	N503
+C01	N701	N504
+D01	N701	N517
+A02	N702	N502
+B02	N702	N503
+C02	N702	N504
+D02	N702	N517
+A03	N703	N502
+B03	N703	N503
+C03	N703	N504
+D03	N703	N517
+A04	N704	N502
+B04	N704	N503
+C04	N704	N504
+D04	N704	N517
+A05	N705	N502
+B05	N705	N503
+C05	N705	N504
+D05	N705	N517
+A06	N706	N502
+B06	N706	N503
+C06	N706	N504
+D06	N706	N517
diff --git a/conf/collection_index_klits/Nextera Index Kit (96 Indexes 384 Samples).txt b/conf/collection_index_klits/Nextera Index Kit (96 Indexes 384 Samples).txt
new file mode 100644
index 00000000..71d2c33b
--- /dev/null
+++ b/conf/collection_index_klits/Nextera Index Kit (96 Indexes 384 Samples).txt	
@@ -0,0 +1,225 @@
+[Version]
+1
+[Name]
+Nextera Index Kit (96 Indexes 384 Samples)
+[PlateExtension]
+nexfc96
+[Settings]
+Adapter	CTGTCTCTTATACACATCT
+[I7]
+N701	TAAGGCGA
+N702	CGTACTAG
+N703	AGGCAGAA
+N704	TCCTGAGC
+N705	GGACTCCT
+N706	TAGGCATG
+N707	CTCTCTAC
+N708	CAGAGAGG
+N709	GCTACGCT
+N710	CGAGGCTG
+N711	AAGAGGCA
+N712	GTAGAGGA
+[I5]
+N501	TAGATCGC
+N502	CTCTCTAT
+N503	TATCCTCT
+N504	AGAGTAGA
+N505	GTAAGGAG
+N506	ACTGCATA
+N507	AAGGAGTA
+N508	CTAAGCCT
+N517	GCGTAAGA
+[DefaultLayout_SingleIndex]
+A01	N701	
+A02	N702	
+A03	N703	
+A04	N704	
+A05	N705	
+A06	N706	
+A07	N707	
+A08	N708	
+A09	N709	
+A10	N710	
+A11	N711	
+A12	N712	
+B01	N701	
+B02	N702	
+B03	N703	
+B04	N704	
+B05	N705	
+B06	N706	
+B07	N707	
+B08	N708	
+B09	N709	
+B10	N710	
+B11	N711	
+B12	N712	
+C01	N701	
+C02	N702	
+C03	N703	
+C04	N704	
+C05	N705	
+C06	N706	
+C07	N707	
+C08	N708	
+C09	N709	
+C10	N710	
+C11	N711	
+C12	N712	
+D01	N701	
+D02	N702	
+D03	N703	
+D04	N704	
+D05	N705	
+D06	N706	
+D07	N707	
+D08	N708	
+D09	N709	
+D10	N710	
+D11	N711	
+D12	N712	
+E01	N701	
+E02	N702	
+E03	N703	
+E04	N704	
+E05	N705	
+E06	N706	
+E07	N707	
+E08	N708	
+E09	N709	
+E10	N710	
+E11	N711	
+E12	N712	
+F01	N701	
+F02	N702	
+F03	N703	
+F04	N704	
+F05	N705	
+F06	N706	
+F07	N707	
+F08	N708	
+F09	N709	
+F10	N710	
+F11	N711	
+F12	N712	
+G01	N701	
+G02	N702	
+G03	N703	
+G04	N704	
+G05	N705	
+G06	N706	
+G07	N707	
+G08	N708	
+G09	N709	
+G10	N710	
+G11	N711	
+G12	N712	
+H01	N701	
+H02	N702	
+H03	N703	
+H04	N704	
+H05	N705	
+H06	N706	
+H07	N707	
+H08	N708	
+H09	N709	
+H10	N710	
+H11	N711	
+H12	N712	
+[DefaultLayout_DualIndex]
+A01	N701	N502
+A02	N702	N502
+A03	N703	N502
+A04	N704	N502
+A05	N705	N502
+A06	N706	N502
+A07	N707	N502
+A08	N708	N502
+A09	N709	N502
+A10	N710	N502
+A11	N711	N502
+A12	N712	N502
+B01	N701	N503
+B02	N702	N503
+B03	N703	N503
+B04	N704	N503
+B05	N705	N503
+B06	N706	N503
+B07	N707	N503
+B08	N708	N503
+B09	N709	N503
+B10	N710	N503
+B11	N711	N503
+B12	N712	N503
+C01	N701	N504
+C02	N702	N504
+C03	N703	N504
+C04	N704	N504
+C05	N705	N504
+C06	N706	N504
+C07	N707	N504
+C08	N708	N504
+C09	N709	N504
+C10	N710	N504
+C11	N711	N504
+C12	N712	N504
+D01	N701	N505
+D02	N702	N505
+D03	N703	N505
+D04	N704	N505
+D05	N705	N505
+D06	N706	N505
+D07	N707	N505
+D08	N708	N505
+D09	N709	N505
+D10	N710	N505
+D11	N711	N505
+D12	N712	N505
+E01	N701	N506
+E02	N702	N506
+E03	N703	N506
+E04	N704	N506
+E05	N705	N506
+E06	N706	N506
+E07	N707	N506
+E08	N708	N506
+E09	N709	N506
+E10	N710	N506
+E11	N711	N506
+E12	N712	N506
+F01	N701	N507
+F02	N702	N507
+F03	N703	N507
+F04	N704	N507
+F05	N705	N507
+F06	N706	N507
+F07	N707	N507
+F08	N708	N507
+F09	N709	N507
+F10	N710	N507
+F11	N711	N507
+F12	N712	N507
+G01	N701	N508
+G02	N702	N508
+G03	N703	N508
+G04	N704	N508
+G05	N705	N508
+G06	N706	N508
+G07	N707	N508
+G08	N708	N508
+G09	N709	N508
+G10	N710	N508
+G11	N711	N508
+G12	N712	N508
+H01	N701	N517
+H02	N702	N517
+H03	N703	N517
+H04	N704	N517
+H05	N705	N517
+H06	N706	N517
+H07	N707	N517
+H08	N708	N517
+H09	N709	N517
+H10	N710	N517
+H11	N711	N517
+H12	N712	N517
diff --git a/conf/collection_index_klits/Nextera XT Index Kit (24 Indexes 96 Samples).txt b/conf/collection_index_klits/Nextera XT Index Kit (24 Indexes 96 Samples).txt
new file mode 100644
index 00000000..46c8c80c
--- /dev/null
+++ b/conf/collection_index_klits/Nextera XT Index Kit (24 Indexes 96 Samples).txt	
@@ -0,0 +1,70 @@
+[Version]
+1
+[Name]
+Nextera XT Index Kit (24 Indexes 96 Samples)
+[PlateExtension]
+nexxt24
+[Settings]
+Adapter	CTGTCTCTTATACACATCT
+[I7]
+N701	TAAGGCGA
+N702	CGTACTAG
+N703	AGGCAGAA
+N704	TCCTGAGC
+N705	GGACTCCT
+N706	TAGGCATG
+[I5]
+S502	CTCTCTAT
+S503	TATCCTCT
+S504	AGAGTAGA
+S517	GCGTAAGA
+[DefaultLayout_SingleIndex]
+A01	N701
+B01	N701
+C01	N701
+D01	N701
+A02	N702
+B02	N702
+C02	N702
+D02	N702
+A03	N703
+B03	N703
+C03	N703
+D03	N703
+A04	N704
+B04	N704
+C04	N704
+D04	N704
+A05	N705
+B05	N705
+C05	N705
+D05	N705
+A06	N706
+B06	N706
+C06	N706
+D06	N706	
+[DefaultLayout_DualIndex]
+A01	N701	S502
+B01	N701	S503
+C01	N701	S504
+D01	N701	S517
+A02	N702	S502
+B02	N702	S503
+C02	N702	S504
+D02	N702	S517
+A03	N703	S502
+B03	N703	S503
+C03	N703	S504
+D03	N703	S517
+A04	N704	S502
+B04	N704	S503
+C04	N704	S504
+D04	N704	S517
+A05	N705	S502
+B05	N705	S503
+C05	N705	S504
+D05	N705	S517
+A06	N706	S502
+B06	N706	S503
+C06	N706	S504
+D06	N706	S517
\ No newline at end of file
diff --git a/conf/collection_index_klits/Nextera XT Index Kit (96 Indexes 384 Samples).txt b/conf/collection_index_klits/Nextera XT Index Kit (96 Indexes 384 Samples).txt
new file mode 100644
index 00000000..2c220d40
--- /dev/null
+++ b/conf/collection_index_klits/Nextera XT Index Kit (96 Indexes 384 Samples).txt	
@@ -0,0 +1,225 @@
+[Version]
+1
+[Name]
+Nextera XT Index Kit (96 Indexes 384 Samples)
+[PlateExtension]
+nexxt96
+[Settings]
+Adapter	CTGTCTCTTATACACATCT
+[I7]
+N701	TAAGGCGA
+N702	CGTACTAG
+N703	AGGCAGAA
+N704	TCCTGAGC
+N705	GGACTCCT
+N706	TAGGCATG
+N707	CTCTCTAC
+N708	CAGAGAGG
+N709	GCTACGCT
+N710	CGAGGCTG
+N711	AAGAGGCA
+N712	GTAGAGGA
+[I5]
+S501	TAGATCGC
+S502	CTCTCTAT
+S503	TATCCTCT
+S504	AGAGTAGA
+S505	GTAAGGAG
+S506	ACTGCATA
+S507	AAGGAGTA
+S508	CTAAGCCT
+S517	GCGTAAGA
+[DefaultLayout_SingleIndex]
+A01	N701	
+A02	N702	
+A03	N703	
+A04	N704	
+A05	N705	
+A06	N706	
+A07	N707	
+A08	N708	
+A09	N709	
+A10	N710	
+A11	N711	
+A12	N712	
+B01	N701	
+B02	N702	
+B03	N703	
+B04	N704	
+B05	N705	
+B06	N706	
+B07	N707	
+B08	N708	
+B09	N709	
+B10	N710	
+B11	N711	
+B12	N712	
+C01	N701	
+C02	N702	
+C03	N703	
+C04	N704	
+C05	N705	
+C06	N706	
+C07	N707	
+C08	N708	
+C09	N709	
+C10	N710	
+C11	N711	
+C12	N712	
+D01	N701	
+D02	N702	
+D03	N703	
+D04	N704	
+D05	N705	
+D06	N706	
+D07	N707	
+D08	N708	
+D09	N709	
+D10	N710	
+D11	N711	
+D12	N712	
+E01	N701	
+E02	N702	
+E03	N703	
+E04	N704	
+E05	N705	
+E06	N706	
+E07	N707	
+E08	N708	
+E09	N709	
+E10	N710	
+E11	N711	
+E12	N712	
+F01	N701	
+F02	N702	
+F03	N703	
+F04	N704	
+F05	N705	
+F06	N706	
+F07	N707	
+F08	N708	
+F09	N709	
+F10	N710	
+F11	N711	
+F12	N712	
+G01	N701	
+G02	N702	
+G03	N703	
+G04	N704	
+G05	N705	
+G06	N706	
+G07	N707	
+G08	N708	
+G09	N709	
+G10	N710	
+G11	N711	
+G12	N712	
+H01	N701	
+H02	N702	
+H03	N703	
+H04	N704	
+H05	N705	
+H06	N706	
+H07	N707	
+H08	N708	
+H09	N709	
+H10	N710	
+H11	N711	
+H12	N712	
+[DefaultLayout_DualIndex]
+A01	N701	S502
+A02	N702	S502
+A03	N703	S502
+A04	N704	S502
+A05	N705	S502
+A06	N706	S502
+A07	N707	S502
+A08	N708	S502
+A09	N709	S502
+A10	N710	S502
+A11	N711	S502
+A12	N712	S502
+B01	N701	S503
+B02	N702	S503
+B03	N703	S503
+B04	N704	S503
+B05	N705	S503
+B06	N706	S503
+B07	N707	S503
+B08	N708	S503
+B09	N709	S503
+B10	N710	S503
+B11	N711	S503
+B12	N712	S503
+C01	N701	S504
+C02	N702	S504
+C03	N703	S504
+C04	N704	S504
+C05	N705	S504
+C06	N706	S504
+C07	N707	S504
+C08	N708	S504
+C09	N709	S504
+C10	N710	S504
+C11	N711	S504
+C12	N712	S504
+D01	N701	S505
+D02	N702	S505
+D03	N703	S505
+D04	N704	S505
+D05	N705	S505
+D06	N706	S505
+D07	N707	S505
+D08	N708	S505
+D09	N709	S505
+D10	N710	S505
+D11	N711	S505
+D12	N712	S505
+E01	N701	S506
+E02	N702	S506
+E03	N703	S506
+E04	N704	S506
+E05	N705	S506
+E06	N706	S506
+E07	N707	S506
+E08	N708	S506
+E09	N709	S506
+E10	N710	S506
+E11	N711	S506
+E12	N712	S506
+F01	N701	S507
+F02	N702	S507
+F03	N703	S507
+F04	N704	S507
+F05	N705	S507
+F06	N706	S507
+F07	N707	S507
+F08	N708	S507
+F09	N709	S507
+F10	N710	S507
+F11	N711	S507
+F12	N712	S507
+G01	N701	S508
+G02	N702	S508
+G03	N703	S508
+G04	N704	S508
+G05	N705	S508
+G06	N706	S508
+G07	N707	S508
+G08	N708	S508
+G09	N709	S508
+G10	N710	S508
+G11	N711	S508
+G12	N712	S508
+H01	N701	S517
+H02	N702	S517
+H03	N703	S517
+H04	N704	S517
+H05	N705	S517
+H06	N706	S517
+H07	N707	S517
+H08	N708	S517
+H09	N709	S517
+H10	N710	S517
+H11	N711	S517
+H12	N712	S517
diff --git a/conf/collection_index_klits/Nextera XT v2 Index Kit A.txt b/conf/collection_index_klits/Nextera XT v2 Index Kit A.txt
new file mode 100644
index 00000000..fd5d306b
--- /dev/null
+++ b/conf/collection_index_klits/Nextera XT v2 Index Kit A.txt	
@@ -0,0 +1,224 @@
+[Version]
+1
+[Name]
+Nextera XT v2 Index Kit A
+[PlateExtension]
+nexxtv2a
+[Settings]
+Adapter	CTGTCTCTTATACACATCT
+[I7]
+N701	TAAGGCGA
+N702	CGTACTAG
+N703	AGGCAGAA
+N704	TCCTGAGC
+N705	GGACTCCT
+N706	TAGGCATG
+N707	CTCTCTAC
+N710	CGAGGCTG
+N711	AAGAGGCA
+N712	GTAGAGGA
+N714	GCTCATGA
+N715	ATCTCAGG
+[I5]
+S502	CTCTCTAT
+S503	TATCCTCT
+S505	GTAAGGAG
+S506	ACTGCATA
+S507	AAGGAGTA
+S508	CTAAGCCT
+S510	CGTCTAAT
+S511	TCTCTCCG
+[DefaultLayout_SingleIndex]
+A01	N701	
+A02	N702	
+A03	N703	
+A04	N704	
+A05	N705	
+A06	N706	
+A07	N707	
+A08	N710	
+A09	N711	
+A10	N712	
+A11	N714	
+A12	N715	
+B01	N701	
+B02	N702	
+B03	N703	
+B04	N704	
+B05	N705	
+B06	N706	
+B07	N707	
+B08	N710	
+B09	N711	
+B10	N712	
+B11	N714	
+B12	N715	
+C01	N701	
+C02	N702	
+C03	N703	
+C04	N704	
+C05	N705	
+C06	N706	
+C07	N707	
+C08	N710	
+C09	N711	
+C10	N712	
+C11	N714	
+C12	N715	
+D01	N701	
+D02	N702	
+D03	N703	
+D04	N704	
+D05	N705	
+D06	N706	
+D07	N707	
+D08	N710	
+D09	N711	
+D10	N712	
+D11	N714	
+D12	N715	
+E01	N701	
+E02	N702	
+E03	N703	
+E04	N704	
+E05	N705	
+E06	N706	
+E07	N707	
+E08	N710	
+E09	N711	
+E10	N712	
+E11	N714	
+E12	N715	
+F01	N701	
+F02	N702	
+F03	N703	
+F04	N704	
+F05	N705	
+F06	N706	
+F07	N707	
+F08	N710	
+F09	N711	
+F10	N712	
+F11	N714	
+F12	N715	
+G01	N701	
+G02	N702	
+G03	N703	
+G04	N704	
+G05	N705	
+G06	N706	
+G07	N707	
+G08	N710	
+G09	N711	
+G10	N712	
+G11	N714	
+G12	N715	
+H01	N701	
+H02	N702	
+H03	N703	
+H04	N704	
+H05	N705	
+H06	N706	
+H07	N707	
+H08	N710	
+H09	N711	
+H10	N712	
+H11	N714	
+H12	N715		
+[DefaultLayout_DualIndex]
+A01	N701	S502	
+A02	N702	S502	
+A03	N703	S502	
+A04	N704	S502	
+A05	N705	S502	
+A06	N706	S502	
+A07	N707	S502	
+A08	N710	S502	
+A09	N711	S502	
+A10	N712	S502	
+A11	N714	S502	
+A12	N715	S502	
+B01	N701	S503	
+B02	N702	S503	
+B03	N703	S503	
+B04	N704	S503	
+B05	N705	S503	
+B06	N706	S503	
+B07	N707	S503	
+B08	N710	S503	
+B09	N711	S503	
+B10	N712	S503	
+B11	N714	S503	
+B12	N715	S503	
+C01	N701	S505	
+C02	N702	S505	
+C03	N703	S505	
+C04	N704	S505	
+C05	N705	S505	
+C06	N706	S505	
+C07	N707	S505	
+C08	N710	S505	
+C09	N711	S505	
+C10	N712	S505	
+C11	N714	S505	
+C12	N715	S505	
+D01	N701	S506	
+D02	N702	S506	
+D03	N703	S506	
+D04	N704	S506	
+D05	N705	S506	
+D06	N706	S506	
+D07	N707	S506	
+D08	N710	S506	
+D09	N711	S506	
+D10	N712	S506	
+D11	N714	S506	
+D12	N715	S506	
+E01	N701	S507	
+E02	N702	S507	
+E03	N703	S507	
+E04	N704	S507	
+E05	N705	S507	
+E06	N706	S507	
+E07	N707	S507	
+E08	N710	S507	
+E09	N711	S507	
+E10	N712	S507	
+E11	N714	S507	
+E12	N715	S507	
+F01	N701	S508	
+F02	N702	S508	
+F03	N703	S508	
+F04	N704	S508	
+F05	N705	S508	
+F06	N706	S508	
+F07	N707	S508	
+F08	N710	S508	
+F09	N711	S508	
+F10	N712	S508	
+F11	N714	S508	
+F12	N715	S508	
+G01	N701	S510	
+G02	N702	S510	
+G03	N703	S510	
+G04	N704	S510	
+G05	N705	S510	
+G06	N706	S510	
+G07	N707	S510	
+G08	N710	S510	
+G09	N711	S510	
+G10	N712	S510	
+G11	N714	S510	
+G12	N715	S510	
+H01	N701	S511	
+H02	N702	S511	
+H03	N703	S511	
+H04	N704	S511	
+H05	N705	S511	
+H06	N706	S511	
+H07	N707	S511	
+H08	N710	S511	
+H09	N711	S511	
+H10	N712	S511	
+H11	N714	S511	
+H12	N715	S511	
\ No newline at end of file
diff --git a/conf/collection_index_klits/TruSeq RNA Single Indexes Set A.txt b/conf/collection_index_klits/TruSeq RNA Single Indexes Set A.txt
new file mode 100644
index 00000000..bb771a32
--- /dev/null
+++ b/conf/collection_index_klits/TruSeq RNA Single Indexes Set A.txt	
@@ -0,0 +1,119 @@
+[Version]
+1
+[Name]
+TruSeq RNA Single Indexes Set A
+[PlateExtension]
+trursinglea
+[Settings]
+Adapter	AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
+AdapterRead2	AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
+[I7]
+AR002	CGATGT
+AR004	TGACCA
+AR005	ACAGTG
+AR006	GCCAAT
+AR007	CAGATC
+AR012	CTTGTA
+AR013	AGTCAA
+AR014	AGTTCC
+AR015	ATGTCA
+AR016	CCGTCC
+AR018	GTCCGC
+AR019	GTGAAA
+[DefaultLayout_SingleIndex]
+A01	AR002	
+A02	AR004	
+A03	AR005	
+A04	AR006	
+A05	AR007	
+A06	AR012	
+A07	AR013	
+A08	AR014	
+A09	AR015	
+A10	AR016	
+A11	AR018	
+A12	AR019	
+B01	AR002	
+B02	AR004	
+B03	AR005	
+B04	AR006	
+B05	AR007	
+B06	AR012	
+B07	AR013	
+B08	AR014	
+B09	AR015	
+B10	AR016	
+B11	AR018	
+B12	AR019	
+C01	AR002	
+C02	AR004	
+C03	AR005	
+C04	AR006	
+C05	AR007	
+C06	AR012	
+C07	AR013	
+C08	AR014	
+C09	AR015	
+C10	AR016	
+C11	AR018	
+C12	AR019	
+D01	AR002	
+D02	AR004	
+D03	AR005	
+D04	AR006	
+D05	AR007	
+D06	AR012	
+D07	AR013	
+D08	AR014	
+D09	AR015	
+D10	AR016	
+D11	AR018	
+D12	AR019	
+E01	AR002	
+E02	AR004	
+E03	AR005	
+E04	AR006	
+E05	AR007	
+E06	AR012	
+E07	AR013	
+E08	AR014	
+E09	AR015	
+E10	AR016	
+E11	AR018	
+E12	AR019	
+F01	AR002	
+F02	AR004	
+F03	AR005	
+F04	AR006	
+F05	AR007	
+F06	AR012	
+F07	AR013	
+F08	AR014	
+F09	AR015	
+F10	AR016	
+F11	AR018	
+F12	AR019	
+G01	AR002	
+G02	AR004	
+G03	AR005	
+G04	AR006	
+G05	AR007	
+G06	AR012	
+G07	AR013	
+G08	AR014	
+G09	AR015	
+G10	AR016	
+G11	AR018	
+G12	AR019	
+H01	AR002	
+H02	AR004	
+H03	AR005	
+H04	AR006	
+H05	AR007	
+H06	AR012	
+H07	AR013	
+H08	AR014	
+H09	AR015	
+H10	AR016	
+H11	AR018	
+H12	AR019	
\ No newline at end of file
diff --git a/install.sh b/install.sh
index b162e10c..b5fd5e2f 100644
--- a/install.sh
+++ b/install.sh
@@ -457,6 +457,10 @@ if [ $upgrade == true ]; then
         cp $INSTALL_PATH/conf/*_template.csv $INSTALL_PATH/documents/wetlab/templates/
         cp $INSTALL_PATH/conf/samples_template.xlsx $INSTALL_PATH/documents/wetlab/templates/
 
+        # Copy the illumina collection index kits
+        mkdir -p $INSTALL_PATH/documents/wetlab/collection_index_kits/
+        cp $INSTALL_PATH/conf/collection_index_kits/*.txt $INSTALL_PATH/documents/wetlab/collection_index_kits/
+
         # update logging configuration file
         cp $INSTALL_PATH/conf/template_logging_config.ini $INSTALL_PATH/wetlab/logging_config.ini
         sed -i "s@INSTALL_PATH@${INSTALL_PATH}@g" $INSTALL_PATH/wetlab/logging_config.ini