Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
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Dec 19, 2022 - Python
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microbiome
Here are 101 public repositories matching this topic...
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
bioinformatics annotation genomics metagenomics microbiome viral-genomics viral-metagenomics metagenome-assembled-genomes
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Jan 22, 2025 - Python
💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
bioinformatics snakemake systems-biology computational-biology metagenomics metabolism microbiome metabolic-models flux-balance-analysis microbial-ecology gut-microbiome mags genome-scale-metabolic-model metagenome-assembled-genomes metabolic-modeling
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Jul 27, 2024 - Python
Qiita - A multi-omics databasing effort
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Jan 21, 2025 - Python
Python package to study microbial communities using metabolic modeling.
python flux community modeling systems-biology biochemistry microbiome hacktoberfest cobra microbiota cobrapy metabolic-models
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Dec 27, 2024 - Python
ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
bioinformatics taxonomy bloom-filter metagenomics genbank microbiome k-mer ncbi refseq minimizers gtdb
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Feb 12, 2024 - Python
DeepMicrobes: taxonomic classification for metagenomics with deep learning
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Sep 17, 2022 - Python
A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
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Jan 18, 2025 - Python
Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TEMPTED), and Compositional Tensor Factorization (CTF) on sparse compositional omics datasets.
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Oct 1, 2024 - Python
Woltka: a versatile meta'omic data classifier
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Oct 8, 2024 - Python
Cross-disease comparison of case-control gut microbiome studies
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Feb 2, 2019 - Python
The Microbiome Interpretable Temporal Rule Engine
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May 26, 2021 - Python
Sample search by metadata and features
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Aug 31, 2023 - Python
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
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Oct 3, 2023 - Python
Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes
bioinformatics nanopore metagenomics pacbio microbial-genomics microbiome long-read-sequencing metagenome-assembled-genomes
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Dec 30, 2024 - Python
AMPtk: Amplicon ToolKit for NGS data (formally UFITS)
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Nov 18, 2023 - Python
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
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Apr 11, 2023 - Python
creating hybrid-gene phylogenetic trees for diversity analyses
python diversity bioinformatics python3 phylogenetic-trees phylogenetics microbiology microbiome fungi fungal microbial-ecology
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Aug 23, 2022 - Python
StaG Metagenomic Workflow Collaboration
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Aug 20, 2024 - Python
National Microbiome Data Collaborative (NMDC) unified data model
metadata schema genomics standards samples proteomics metabolomics microbiome transcriptomics fair-data ecoinformatics nmdc mixs linkml microbiomedata
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Jan 24, 2025 - Python
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