bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.
☆140Aug 6, 2026Updated last month
Alternatives and similar repositories for biobakery_workflows
Users that are interested in biobakery_workflows are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- bioBakery tools for meta'omic profiling☆324Aug 4, 2026Updated last month
- MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data☆423Sep 10, 2026Updated 2 weeks ago
- MaAsLin2: Microbiome Multivariate Association with Linear Models☆154Feb 5, 2026Updated 7 months ago
- Precise phylogenetic analysis of microbial isolates and genomes from metagenomes☆171Jun 10, 2026Updated 3 months ago
- HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).☆252Sep 2, 2026Updated 3 weeks ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.☆155Jul 11, 2026Updated 2 months ago
- motus - a tool for marker gene-based OTU (mOTU) profiling☆187Jul 17, 2026Updated 2 months ago
- R package for microbiome biomarker discovery☆200Feb 19, 2025Updated last year
- This is the supplementary code for CRC-multi-kingdom☆17Nov 8, 2021Updated 4 years ago
- Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes☆342Updated this week
- hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance☆23Mar 8, 2024Updated 2 years ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆21Aug 13, 2026Updated last month
- KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files☆384Aug 1, 2025Updated last year
- This repository contains computer codes for main analyses of the manuscript titled 'Multi-omic Landscape of Airway Microbe-Host Interacti…☆35Aug 16, 2022Updated 4 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Interpretation and visualization of microbiome charts☆551Jul 22, 2025Updated last year
- Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host…☆26Aug 20, 2026Updated last month
- microbiome R package☆319Sep 8, 2026Updated 2 weeks ago
- A companion R package for the MicrobiomeAnalyst web server☆132Updated this week
- An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within micro…☆274May 13, 2026Updated 4 months ago
- ATLAS - Three commands to start analyzing your metagenome data☆406May 28, 2026Updated 3 months ago
- CAMISIM: Simulating metagenomes and microbial communities☆234Jul 16, 2026Updated 2 months ago
- Making whole bacterial genome sequencing data analysis easy☆116Apr 22, 2025Updated last year
- REference Sequence annotation and CuRatIon Pipeline☆102Updated this week
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Profiler for metagenomics based on NGLess☆14Feb 22, 2024Updated 2 years ago
- High-quality circular representations of taxonomic and phylogenetic trees☆112Aug 7, 2024Updated 2 years ago
- Analysing Metagenomic Species (MGS)☆42Nov 12, 2020Updated 5 years ago
- strain-level analysis tools☆41Oct 21, 2024Updated last year
- A comprehensive R package for deep mining microbiome☆195Apr 29, 2026Updated 4 months ago
- ☆158Dec 30, 2025Updated 8 months ago
- A flexible pipeline for complete analysis of bacterial genomes☆522Aug 5, 2026Updated last month
- AnADAMA2 is the next generation of AnADAMA (Another Automated Data Analysis Management Application). AnADAMA is a tool to capture your wo…☆12Mar 25, 2026Updated 5 months ago
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆681Aug 7, 2026Updated last month
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Microbiome Protocol eBook related documents and scripts.☆49Jun 11, 2021Updated 5 years ago
- Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…☆433Updated this week
- High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers☆46Apr 8, 2024Updated 2 years ago
- Bioinformatics program inStrain☆193Mar 12, 2026Updated 6 months ago
- An updated pipeline for pangenome investigation☆377Jul 2, 2026Updated 2 months ago
- MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis☆477Updated this week
- MGnify genome analysis pipeline☆115Sep 9, 2026Updated 2 weeks ago