Microbiota dedicated tools¶
Metagenomics data manipulation¶
| Name | Version | Galaxy wrapper |
|---|---|---|
| VSEARCH [13] | 1.9.7 | vsearch |
| Nonpareil [11] | 3.1.1 | nonpareil |
Assembly¶
| Name | Version | Galaxy wrapper |
|---|---|---|
| MEGAHIT [7] | 1.1.2 | vsearch |
| metaSPAdes [9] | 3.9.0 | nonpareil |
| metaQUAST [8] | 4.5 | quast |
| VALET | 1.0 | valet |
Metataxonomic sequence analysis¶
| Name | Version | Galaxy wrapper |
|---|---|---|
| Mothur [13] | 1.36.1 | suite_mothur |
| QIIME [4] | 1.9.1 | suite_qiime |
Taxonomy assignation on WGS sequences¶
| Name | Version | Galaxy wrapper |
|---|---|---|
| MetaPhlAn2 [15] | 2.6.0 | suite_metaphlan2 |
| Format MetaPhlAn2 | 0.1.0 | format_metaphlan2_output |
| KRAKEN [15] | 0.10.5 | suite_kraken_0_10_5 |
Metabolism assignation¶
| Name | Version | Galaxy wrapper |
|---|---|---|
| HUMAnN2 [1] | 0.11.1 | suite_humann2 |
| Group HUMAnN2 to GO slim term [3] | 1.2.0 | group_humann2_uniref_abundances_to_go |
| PICRUST [6] | 1.1.1 | suite_picrust |
| InterProScan [5] | 5.0.0 | interproscan5 |
Combination of functional and taxonomic results¶
| Name | Version | Galaxy wrapper |
|---|---|---|
| Combine MetaPhlAn2 and HUMAnN2 outputs | 0.1.0 | combine_metaphlan2_humann2 |
Visualization
| Name | Version | Galaxy wrapper |
|---|---|---|
| export2graphlan | 0.19 | export2graphlan |
| GraPhlAn [2] | 1.0.0 | suite_graphlan |
| KRONA [11] | 2.6.1 | taxonomy_krona_chart |
References
| [1] | Sahar Abubucker, Nicola Segata, Johannes Goll, Alyxandria M. Schubert, Jacques Izard, Brandi L. Cantarel, Beltran Rodriguez-Mueller, Jeremy Zucker, Mathangi Thiagarajan, Bernard Henrissat, Owen White, Scott T. Kelley, Barbara Methé, Patrick D. Schloss, Dirk Gevers, Makedonka Mitreva, and Curtis Huttenhower. Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome. PLoS Comput Biol, 8(6):e1002358, June 2012. URL: http://dx.doi.org/10.1371/journal.pcbi.1002358, doi:10.1371/journal.pcbi.1002358. |
| [2] | Francesco Asnicar, George Weingart, Timothy L Tickle, Curtis Huttenhower, and Nicola Segata. Compact graphical representation of phylogenetic data and metadata with graphlan. PeerJ, 3:e1029, 2015. |
| [3] | Bérénice Batut. Group abundances of UniRef50 gene families obtained with HUMAnN2 to Gene Ontology (GO) slim terms with relative abundances: release v1.2.0. 2016. URL: http://dx.doi.org/10.5281/zenodo.50086. |
| [4] | J. Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D. Bushman, Elizabeth K. Costello, Noah Fierer, Antonio Gonzalez Peña, Julia K. Goodrich, Jeffrey I. Gordon, Gavin A. Huttley, Scott T. Kelley, Dan Knights, Jeremy E. Koenig, Ruth E. Ley, Catherine A. Lozupone, Daniel McDonald, Brian D. Muegge, Meg Pirrung, Jens Reeder, Joel R. Sevinsky, Peter J. Turnbaugh, William A. Walters, Jeremy Widmann, Tanya Yatsunenko, Jesse Zaneveld, and Rob Knight. QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7(5):335–336, May 2010. URL: http://www.nature.com/nmeth/journal/v7/n5/full/nmeth.f.303.html, doi:10.1038/nmeth.f.303. |
| [5] | Sarah Hunter, Rolf Apweiler, Teresa K Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Ujjwal Das, Louise Daugherty, Lauranne Duquenne, and others. Interpro: the integrative protein signature database. Nucleic acids research, 37(suppl_1):D211–D215, 2008. |
| [6] | Morgan GI Langille, Jesse Zaneveld, J Gregory Caporaso, Daniel McDonald, Dan Knights, Joshua A Reyes, Jose C Clemente, Deron E Burkepile, Rebecca L Vega Thurber, Rob Knight, and others. Predictive functional profiling of microbial communities using 16s rrna marker gene sequences. Nature biotechnology, 31(9):814–821, 2013. |
| [7] | Dinghua Li, Chi-Man Liu, Ruibang Luo, Kunihiko Sadakane, and Tak-Wah Lam. Megahit: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de bruijn graph. Bioinformatics, 31(10):1674–1676, 2015. |
| [8] | Alla Mikheenko, Vladislav Saveliev, and Alexey Gurevich. Metaquast: evaluation of metagenome assemblies. Bioinformatics, 32(7):1088–1090, 2015. |
| [9] | Sergey Nurk, Dmitry Meleshko, Anton Korobeynikov, and Pavel Pevzner. Metaspades: a new versatile de novo metagenomics assembler. arXiv preprint arXiv:1604.03071, 2016. |
| [11] | Brian D Ondov, Nicholas H Bergman, and Adam M Phillippy. Interactive metagenomic visualization in a web browser. BMC bioinformatics, 12(1):385, 2011. |
| [11] | Luis M Rodriguez-r and Konstantinos T Konstantinidis. Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets. Bioinformatics, 30(5):629–635, 2013. |
| [13] | Torbjørn Rognes, Frédéric Mahé, Tomas Flouri, Daniel McDonal, and Pat Schloss. Vsearch: VSEARCH 1.4.0. 2015. URL: https://github.com/torognes/vsearch. |
| [13] | Patrick D. Schloss, Sarah L. Westcott, Thomas Ryabin, Justine R. Hall, Martin Hartmann, Emily B. Hollister, Ryan A. Lesniewski, Brian B. Oakley, Donovan H. Parks, Courtney J. Robinson, Jason W. Sahl, Blaz Stres, Gerhard G. Thallinger, David J. Van Horn, and Carolyn F. Weber. Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities. Appl. Environ. Microbiol., 75(23):7537–7541, December 2009. URL: http://aem.asm.org/content/75/23/7537, doi:10.1128/AEM.01541-09. |
| [15] | Duy Tin Truong, Eric A. Franzosa, Timothy L. Tickle, Matthias Scholz, George Weingart, Edoardo Pasolli, Adrian Tett, Curtis Huttenhower, and Nicola Segata. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Meth, 12(10):902–903, October 2015. URL: http://www.nature.com.gate1.inist.fr/nmeth/journal/v12/n10/full/nmeth.3589.html, doi:10.1038/nmeth.3589. |
| [15] | Derrick E Wood and Steven L Salzberg. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome biology, 15(3):R46, 2014. |
