Merge pull request #3152 from yvanlebras/obitools

CONTRIBUTORS.yaml

@@ -349,6 +349,11 @@ EngyNasr:
     gitter: EngyNasr
     joined: 2021-05
 
+ecoissac:
+    github: false
+    name: Eric Coissac
+    joined: 2022-02
+
 erxleben:
     name: Anika Erxleben
     email: anikaerxleben@gmail.com
@@ -400,6 +405,11 @@ fpsom:
     linkedin: fpsom
     joined: 2019-03
 
+fboyer:
+    github: false
+    name: Frédéric Boyer
+    joined: 2022-02
+
 fmareuil:
     name: Fabien Mareuil
     joined: 2017-09

topics/ecology/tutorials/Obitools-metabarcoding/data-library.yaml

@@ -0,0 +1,12 @@
+---
+destination:
+  type: library
+  name: GTN - Material
+  description: Galaxy Training Network Material
+  synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
+items:
+- name: New topic
+  description: Topic summary
+  items:
+  - name: Metabarcoding/eDNA through Obitools
+    items: []

topics/ecology/tutorials/Obitools-metabarcoding/tutorial.bib

@@ -0,0 +1,144 @@
+
+# This is the bibliography file for your tutorial.
+#
+# To add bibliography (bibtex) entries here, follow these steps:
+#  1) Find the DOI for the article you want to cite
+#  2) Go to https://doi2bib.org and fill in the DOI
+#  3) Copy the resulting bibtex entry into this file
+#
+# To cite the example below, in your tutorial.md file
+# use {% cite Batut2018 %}
+#
+# If you want to cite an online resourse (website etc)
+# you can use the 'online' format (see below)
+#
+# You can remove the examples below
+
+@article{Shehzad2012,
+  doi = {10.1111/j.1365-294x.2011.05424.x},
+  url = {https://doi.org/10.1111/j.1365-294x.2011.05424.x},
+  year = {2012},
+  month = jan,
+  publisher = {Wiley},
+  volume = {21},
+  number = {8},
+  pages = {1951--1965},
+  author = {WASIM SHEHZAD and TIAYYBA RIAZ and MUHAMMAD A. NAWAZ and CHRISTIAN MIQUEL and CAROLE POILLOT and SAFDAR A. SHAH and FRAN{\c{C}}OIS POMPANON and ERIC COISSAC and PIERRE TABERLET},
+  title = {Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan},
+  journal = {Molecular Ecology}
+}
+
+@ARTICLE{Caporaso2010,
+  title     = "{QIIME} allows analysis of high-throughput community sequencing
+               data",
+  author    = "Caporaso, J Gregory and Kuczynski, Justin and Stombaugh, Jesse
+               and Bittinger, Kyle and Bushman, Frederic D and Costello,
+               Elizabeth K and Fierer, Noah and Pe{\~n}a, Antonio Gonzalez and
+               Goodrich, Julia K and Gordon, Jeffrey I and Huttley, Gavin A and
+               Kelley, Scott T and Knights, Dan and Koenig, Jeremy E and Ley,
+               Ruth E and Lozupone, Catherine A and McDonald, Daniel and
+               Muegge, Brian D and Pirrung, Meg and Reeder, Jens and Sevinsky,
+               Joel R and Turnbaugh, Peter J and Walters, William A and
+               Widmann, Jeremy and Yatsunenko, Tanya and Zaneveld, Jesse and
+               Knight, Rob",
+  journal   = "Nat. Methods",
+  publisher = "Springer Science and Business Media LLC",
+  volume    =  7,
+  number    =  5,
+  pages     = "335--336",
+  month     =  may,
+  year      =  2010,
+  language  = "en"
+}
+
+
+@ARTICLE{Schloss2009,
+  title     = "Introducing mothur: open-source, platform-independent,
+               community-supported software for describing and comparing
+               microbial communities",
+  author    = "Schloss, Patrick D and Westcott, Sarah L and Ryabin, Thomas and
+               Hall, Justine R and Hartmann, Martin and Hollister, Emily B and
+               Lesniewski, Ryan A and Oakley, Brian B and Parks, Donovan H and
+               Robinson, Courtney J and Sahl, Jason W and Stres, Blaz and
+               Thallinger, Gerhard G and Van Horn, David J and Weber, Carolyn F",
+  abstract  = "mothur aims to be a comprehensive software package that allows
+               users to use a single piece of software to analyze community
+               sequence data. It builds upon previous tools to provide a
+               flexible and powerful software package for analyzing sequencing
+               data. As a case study, we used mothur to trim, screen, and align
+               sequences; calculate distances; assign sequences to operational
+               taxonomic units; and describe the alpha and beta diversity of
+               eight marine samples previously characterized by pyrosequencing
+               of 16S rRNA gene fragments. This analysis of more than 222,000
+               sequences was completed in less than 2 h with a laptop computer.",
+  journal   = "Appl. Environ. Microbiol.",
+  publisher = "American Society for Microbiology",
+  volume    =  75,
+  number    =  23,
+  pages     = "7537--7541",
+  month     =  dec,
+  year      =  2009,
+  language  = "en"
+}
+
+@article{Seguritan2001,
+  doi = {10.1186/1471-2105-2-9},
+  url = {https://doi.org/10.1186/1471-2105-2-9},
+  year = {2001},
+  month = feb,
+  publisher = {Springer Nature},
+  volume = {2},
+  pages = {9},
+  author = {V Seguritan and F Rohwer},
+  title = {FastGroup: a program to dereplicate libraries of 16S rDNA sequences},
+  journal = {BMC Bioinformatics}
+}
+
+@article{Riaz2011,
+  doi = {10.1093/nar/gkr732},
+  url = {https://doi.org/10.1093/nar/gkr732},
+  year = {2011},
+  month = sep,
+  publisher = {Oxford University Press ({OUP})},
+  volume = {39},
+  number = {21},
+  pages = {e145--e145},
+  author = {Tiayyba Riaz and Wasim Shehzad and Alain Viari and Fran{\c{c}}ois Pompanon and Pierre Taberlet and Eric Coissac},
+  title = {{ecoPrimers}: inference of new {DNA} barcode markers from whole genome sequence analysis},
+  journal = {Nucleic Acids Research}
+}
+
+@article{Ficetola2010,
+  doi = {10.1186/1471-2164-11-434},
+  url = {https://doi.org/10.1186/1471-2164-11-434},
+  year = {2010},
+  month = jul,
+  publisher = {Oxford University Press ({OUP})},
+  volume = {39},
+  number = {21},
+  pages = {e145--e145},
+  author = {Gentile Francesco Ficetola and Eric Coissac and Stéphanie Zundel and Tiayyba Riaz and Wasim Shehzad and Julien Bessière and Pierre Taberlet and Fran{\c{c}}ois Pompanon},
+  title = {An In silico approach for the evaluation of DNA barcodes},
+  journal = {BMC Genomics}
+}
+
+@article{Boyer2015,
+  doi = {10.1111/1755-0998.12428},
+  url = {https://doi.org/10.1111/1755-0998.12428},
+  year = {2015},
+  month = may,
+  publisher = {Wiley},
+  volume = {16},
+  number = {1},
+  pages = {176--182},
+  author = {Fr{\'{e}}d{\'{e}}ric Boyer and C{\'{e}}line Mercier and Aur{\'{e}}lie Bonin and Yvan Le Bras and Pierre Taberlet and Eric Coissac},
+  title = {obitools: aunix-inspired software package for {DNA} metabarcoding},
+  journal = {Molecular Ecology Resources}
+}
+
+@online{gtn-website,
+  author = {GTN community},
+  title = {GTN Training Materials: Collection of tutorials developed and maintained by the worldwide Galaxy community},
+  url = {https://training.galaxyproject.org},
+  urldate = {2021-03-24}
+}