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1. biobakery_workflows biobakery_workflows Public

   bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.

   Python 101 33

2. humann humann Public

   HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

   Python 167 58

3. MetaPhlAn MetaPhlAn Public

   MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

   Python 295 85

4. phylophlan phylophlan Public

   Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

   Python 123 33

5. Maaslin2 Maaslin2 Public

   MaAsLin2: Microbiome Multivariate Association with Linear Models

   R 114 35

6. kneaddata kneaddata Public

   Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.

   Python 106 28