Merge pull request galaxyproject#4965 from bebatut/dada2-tutorial

Add DADA2 tutorial

topics/microbiome/tutorials/dada-16S/faqs/index.md

@@ -0,0 +1,3 @@
+---
+layout: faq-page
+---

topics/microbiome/tutorials/dada-16S/tutorial.bib

@@ -0,0 +1,157 @@
+
+# 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{_zkurt_2022,
+	author = {{\" O}zkurt, Ezgi and Fritscher, Joachim and Soranzo, Nicola and Ng, Duncan Y. K. and Davey, Robert P. and Bahram, Mohammad and Hildebrand, Falk},
+	journal = {Microbiome},
+	number = {1},
+	year = {2022},
+	month = {10},
+	publisher = {Springer Science},
+	title = {LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis},
+	volume = {10},
+	doi={10.1186/s40168-022-01365-1}
+}
+
+@article{Andersen_2018,
+	author = {Andersen, Kasper S. and Kirkegaard, Rasmus H. and Karst, S\o{}ren M. and Albertsen, Mads},
+	year = {2018},
+	month = {4},
+	publisher = {Cold Spring Harbor Laboratory},
+	title = {ampvis2: an {R} package to analyse and visualise 16S {rRNA} amplicon data},
+	doi={10.1101/299537}
+}
+
+@article{Bolyen_2019,
+	author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R. and Bokulich, Nicholas A. and Abnet, Christian C. and Al-Ghalith, Gabriel A. and Alexander, Harriet and Alm, Eric J. and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E. and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J. and Brown, C. Titus and Callahan, Benjamin J. and Caraballo-Rodr\i{{\' }}guez, Andr{\' e}s Mauricio and Chase, John and Cope, Emily K. and Silva, Ricardo Da and Diener, Christian and Dorrestein, Pieter C. and Douglas, Gavin M. and Durall, Daniel M. and Duvallet, Claire and Edwardson, Christian F. and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M. and Gibbons, Sean M. and Gibson, Deanna L. and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin A. and Janssen, Stefan and Jarmusch, Alan K. and Jiang, Lingjing and Kaehler, Benjamin D. and Kang, Kyo Bin and Keefe, Christopher R. and Keim, Paul and Kelley, Scott T. and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan G. I. and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan D. and McDonald, Daniel and McIver, Lauren J. and Melnik, Alexey V. and Metcalf, Jessica L. and Morgan, Sydney C. and Morton, Jamie T. and Naimey, Ahmad Turan and Navas-Molina, Jose A. and Nothias, Louis Felix and Orchanian, Stephanie B. and Pearson, Talima and Peoples, Samuel L. and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, Michael S. and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R. and Swafford, Austin D. and Thompson, Luke R. and Torres, Pedro J. and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J. and Ul-Hasan, Sabah and van der Hooft, Justin J. J. and Vargas, Fernando and V{\' a}zquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C. and Williamson, Charles H. D. and Willis, Amy D. and Xu, Zhenjiang Zech and Zaneveld, Jesse R. and Zhang, Yilong and Zhu, Qiyun and Knight, Rob and Caporaso, J. Gregory},
+	journal = {Nature Biotechnology},
+	number = {8},
+	year = {2019},
+	month = {7},
+	pages = {852--857},
+	publisher = {Springer Science},
+	title = {Reproducible, interactive, scalable and extensible microbiome data science using {QIIME} 2},
+	volume = {37},
+	doi= {10.1038/s41587-019-0209-9}
+}
+
+@article{Callahan_2016,
+	author = {Callahan, Benjamin J and McMurdie, Paul J and Rosen, Michael J and Han, Andrew W and Johnson, Amy Jo A and Holmes, Susan P},
+	journal = {Nature Methods},
+	number = {7},
+	year = {2016},
+	month = {5},
+	pages = {581--583},
+	publisher = {Springer Science},
+	title = {DADA2: High-resolution sample inference from {Illumina} amplicon data},
+	volume = {13},
+	doi= {10.1038/nmeth.3869}
+}
+
+@article{edgar2018updating,
+  title={Updating the 97\% identity threshold for 16S ribosomal RNA OTUs},
+  author={Edgar, Robert C},
+  journal={Bioinformatics},
+  volume={34},
+  number={14},
+  pages={2371--2375},
+  year={2018},
+  publisher={Oxford University Press},
+  doi={10.1093/bioinformatics/bty113}
+}
+
+@article{McMurdie_2013,
+	author = {McMurdie, Paul J. and Holmes, Susan},
+	journal = {PLoS ONE},
+	editor = {Watson, Michael},
+	number = {4},
+	year = {2013},
+	month = {4},
+	pages = {e61217},
+	publisher = {Public Library of Science (PLoS)},
+	title = {phyloseq: An {R} {Package} for {Reproducible} {Interactive} {Analysis} and {Graphics} of {Microbiome} {Census} {Data}},
+	volume = {8},
+	doi={10.1371/journal.pone.0061217}
+}
+
+@article{mcmurdie2015shiny,
+  title={Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking},
+  author={McMurdie, Paul J and Holmes, Susan},
+  journal={Bioinformatics},
+  volume={31},
+  number={2},
+  pages={282--283},
+  year={2015},
+  publisher={Oxford University Press},
+  doi={10.1093/bioinformatics/btu616}
+}
+
+
+@article{Schloss_2009,
+	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 Horn, David J. Van and Weber, Carolyn F.},
+	journal = {Applied and Environmental Microbiology},
+	number = {23},
+	year = {2009},
+	month = {10},
+	pages = {7537--7541},
+	publisher = {American Society for Microbiology},
+	title = {Introducing mothur: Open-{Source}, {Platform}-{Independent}, {Community}-{Supported} {Software} for {Describing} and {Comparing} {Microbial} {Communities}},
+	volume = {75},
+    doi={10.1128/aem.01541-09}
+}
+
+@article{Shannon.1948,
+	author = {Shannon, C. E.},
+	year = {1948},
+	title = {A Mathematical Theory of Communication},
+	pages = {379--423},
+	volume = {27},
+	number = {3},
+	issn = {00058580},
+	journal = {Bell System Technical Journal},
+	doi = {10.1002/j.1538-7305.1948.tb01338.x}
+}
+
+
+@article{SIMPSON.1949,
+	author = {SIMPSON, E. H.},
+	year = {1949},
+	title = {Measurement of Diversity},
+	pages = {688},
+	volume = {163},
+	number = {4148},
+	issn = {0028-0836},
+	journal = {Nature},
+	doi = {10.1038/163688a0}
+}
+
+@article{Wang_2007,
+	author = {Wang, Qiong and Garrity, George M. and Tiedje, James M. and Cole, James R.},
+	journal = {Applied and Environmental Microbiology},
+	number = {16},
+	year = {2007},
+	month = {6},
+	pages = {5261--5267},
+	publisher = {American Society for Microbiology},
+	title = {Nai{\` {I}}ve {Bayesian} {Classifier} for {Rapid} {Assignment} of {rRNA} {Sequences} into the {New} {Bacterial} {Taxonomy}},
+	volume = {73},
+	doi = {10.1128/aem.00062-07}
+}
+
+
+