bioBakery

Software, documentation, and tutorials for microbial community profiling.

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biobakery_workflowsbiobakery_workflowsPublic
bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.
Python 110 34
humannhumannPublic
HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).
Python 189 63
MetaPhlAnMetaPhlAnPublic
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
Python 331 88
phylophlanphylophlanPublic
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
Python 136 33
Maaslin2Maaslin2Public
MaAsLin2: Microbiome Multivariate Association with Linear Models
R 134 35
kneaddatakneaddataPublic
Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
Python 116 31

Repositories

Showing 10 of 126 repositories

fugassem Public
FUGAsseM: Function predictor of Uncharacterized Gene products by Assessing high-dimensional community data in Microbiomes
biobakery/fugassem’s past year of commit activity
Python 30 2 0 UpdatedMar 29, 2025
conda-biobakery Public
A collection of conda build recipes
biobakery/conda-biobakery’s past year of commit activity
Shell 2 1 0 0 UpdatedMar 27, 2025
biobakery Public
bioBakery tools for meta'omic profiling
biobakery/biobakery’s past year of commit activity
Shell 272 75 39 1 UpdatedMar 26, 2025
baqlava Public
Bioinformatic Application for Quantification and LAbeling of VirAl taxonomy
biobakery/baqlava’s past year of commit activity
Python 30 0 0 UpdatedMar 26, 2025
maaslin3 Public
MaAsLin3: Microbiome Multivariate Association with Linear Models
biobakery/maaslin3’s past year of commit activity
R 32 1 0 0 UpdatedMar 26, 2025
maaslin3_lite Public
Lefse like wrapper for MaAsLin3
biobakery/maaslin3_lite’s past year of commit activity
ReScript 10 0 0 UpdatedMar 25, 2025
kneaddata Public
Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
biobakery/kneaddata’s past year of commit activity
Python 116 31 1 12 UpdatedMar 21, 2025
MetaPhlAn Public
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
biobakery/MetaPhlAn’s past year of commit activity
Python 331MIT 88 0 4 UpdatedMar 19, 2025
maaslin3_tutorial_files Public
Outputs files for the MaAsLin 3 tutorial
biobakery/maaslin3_tutorial_files’s past year of commit activity
10 0 0 UpdatedMar 5, 2025
parathaa Public
Preserving and Assimilating Region-specific Ambiguities in Taxonomic Hierarchical Assignments for Amplicons (Parathaa)
biobakery/parathaa’s past year of commit activity
R 30 0 0 UpdatedMar 4, 2025