| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Software and algorithms | ||
| Meteor | (N. Pons et al., 2010, JOBIM, conference); (Wen et al., 2017) | https://www.academia.edu/14061278/METEOR_a_plateform_for_quantitative_metagenomic_profiling_of_complex_ecosystems |
| Trimmomatic | (Bolger et al., 2014) | http://www.usadellab.org/cms/?page=trimmomatic |
| Bowtie2 | (Langmead and Salzberg, 2012) | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Integrated Gut Catalog version 2 (IGC2) | (Wen et al., 2017) | https://data.inrae.fr/dataset.xhtml?persistentId=doi:10.15454/QVCYRB |
| MetaOMineR | (Le Chatelier et al., 2013a) | https://cran.r-project.org/web/packages/momr/index.html |
| KEGG | (Kanehisa et al., 2017) | https://www.genome.jp/kegg/ |
| KBase | (Arkin et al., 2018) | https://www.kbase.us |
| COnstraint-Based Reconstruction and Analysis (COBRA) Toolbox (v2.0) | (Schellenberger et al., 2011) | https://opencobra.github.io/cobratoolbox/stable/index.html |
| MIGRENE Toolbox | (Bidkhori et al., 2021) | https://github.com/sysbiomelab/MIGRENE |
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