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Spades 3.12 #114

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merged 4 commits into from
Jun 1, 2018
Merged

Spades 3.12 #114

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421c4f2
added spades 3.12
SilasK May 31, 2018
9247476
corrected bugs- tested on spades and megahit
SilasK May 31, 2018
3f63fa4
added loose parameters
SilasK Jun 1, 2018
de8c3e6
corrected bug with rel paths
SilasK Jun 1, 2018
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31 changes: 22 additions & 9 deletions atlas/default_values.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,8 +27,11 @@
DUPLICATES_ALLOW_SUBSTITUTIONS = 2

NORMALIZATION_KMER_LENGTH = 21
NORMALIZATION_TARGET_DEPTH = 100
NORMALIZATION_MINIMUM_KMERS = 15

# almost no filtering unless grossly over-represented
NORMALIZATION_TARGET_DEPTH = 10000 #500
# allow very low represented kmers to remain
NORMALIZATION_MINIMUM_KMERS = 3 #15

ASSEMBLY_MEMORY = 50
ASSEMBLY_THREADS = 8
Expand All @@ -40,13 +43,16 @@
MEGAHIT_PRUNE_LEVEL = 2
MEGAHIT_LOW_LOCAL_RATIO = 0.2
SPADES_K = "auto"
PREFILTER_MINIMUM_CONTIG_LENGTH = 500
MINIMUM_CONTIG_LENGTH = 2200

MINIMUM_AVERAGE_COVERAGE = 5
MINIMUM_PERCENT_COVERED_BASES = 40
# basically no filtering after assembly
PREFILTER_MINIMUM_CONTIG_LENGTH = 200 #500
# this is bumped up slightly to filter non-merged R1 and R2 sequences
MINIMUM_CONTIG_LENGTH = 300 #2200

# leave all contigs
MINIMUM_AVERAGE_COVERAGE = 1 #5
MINIMUM_PERCENT_COVERED_BASES = 20 #40
MINIMUM_MAPPED_READS = 0
CONTIG_TRIM_BP = 100
CONTIG_TRIM_BP = 0 #100

# bases
MINIMUM_REGION_OVERLAP = 1
Expand Down Expand Up @@ -106,7 +112,7 @@ def make_default_config():

conf["deduplicate"] = True
conf["error_correction_overlapping_pairs"] = True
conf["merge_pairs_before_assembly"] = True


conf["contaminant_max_indel"] = CONTAMINANT_MAX_INDEL
conf["contaminant_min_ratio"] = CONTAMINANT_MIN_RATIO
Expand All @@ -117,10 +123,15 @@ def make_default_config():
conf["duplicates_only_optical"] = DUPLICATES_ONLY_OPTICAL
conf["duplicates_allow_substitutions"] = DUPLICATES_ALLOW_SUBSTITUTIONS


conf["normalize_reads_before_assembly"] = True
conf["normalization_kmer_length"] = NORMALIZATION_KMER_LENGTH
conf["normalization_target_depth"] = NORMALIZATION_TARGET_DEPTH
conf["normalization_minimum_kmers"] = NORMALIZATION_MINIMUM_KMERS

conf["error_correction_before_assembly"] = True

conf["merge_pairs_before_assembly"] = True
conf["merging_k"] = MERGING_K
conf["merging_extend2"] = MERGING_EXTEND2
conf["merging_flags"] = MERGING_FLAGS
Expand All @@ -140,6 +151,8 @@ def make_default_config():
conf["prefilter_minimum_contig_length"] = PREFILTER_MINIMUM_CONTIG_LENGTH
conf["spades_k"] = SPADES_K
conf["spades_preset"] = 'meta'
conf["spades_skip_BayesHammer"] = False
conf["filter_contigs"] = True
conf["minimum_average_coverage"] = MINIMUM_AVERAGE_COVERAGE
conf["minimum_percent_covered_bases"] = MINIMUM_PERCENT_COVERED_BASES
conf["minimum_mapped_reads"] = MINIMUM_MAPPED_READS
Expand Down
2 changes: 1 addition & 1 deletion atlas/envs/required_packages.yaml
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Expand Up @@ -15,6 +15,6 @@ dependencies:
- prokka=1.12
- pyyaml=3.12
- samtools=1.3.1
- spades=3.11.0
- spades=3.12.0
- sqlite=3.13.0
- subread=1.5.3
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