The Metagenomics-Toolkit is a scalable, data agnostic workflow that automates the analysis of short and long metagenomic reads obtained from Illumina or Oxford Nanopore Technology devices, respectively.
☆28Oct 9, 2026Updated this week
Alternatives and similar repositories for metagenomics-tk
Users that are interested in metagenomics-tk are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A Python package for obtaining, parsing and exploring biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)☆53May 5, 2026Updated 5 months ago
- BiBiGrid is a tool for an easy cluster setup inside a cloud environment.☆18Updated this week
- Utility to analyse a group of closely related MAgs/Genomes/bins/SUBs of more or less dubious origin☆15Sep 24, 2024Updated 2 years ago
- 🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs☆67Aug 28, 2026Updated last month
- Protocol for finding informative protein families and then using them to score omic samples☆19Jul 27, 2022Updated 4 years ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.☆234May 9, 2026Updated 5 months ago
- A Nextflow pipeline designed to classify, align and assemble nanopore metagenomic reads.☆18Mar 18, 2025Updated last year
- ☆15Oct 14, 2023Updated 2 years ago
- ☆11Jan 20, 2022Updated 4 years ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆34Dec 4, 2025Updated 10 months ago
- Hydrocarbon biodegradation gene annotation☆19Jul 14, 2022Updated 4 years ago
- ☆11May 14, 2025Updated last year
- A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.☆20Aug 7, 2026Updated 2 months ago
- k-mer-based non-Bayesian Taxonomic Classifier☆20May 28, 2026Updated 4 months ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- A high-resolution long-read metagenome assembler for even noisy reads. Myloasm assembles strain-resolved, circular + complete genomes fro…☆173Updated this week
- Grabbing genome accessions & download info based on taxonomy, using the NCBI REST API, w00t☆12Feb 23, 2025Updated last year
- Rapid & standardized genome annotation using protein structural information☆81Sep 16, 2026Updated 3 weeks ago
- MetagenOmic read Re-Assigner and abundance quantifier☆22Jun 24, 2026Updated 3 months ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆38Jun 4, 2026Updated 4 months ago
- ☆10Jun 9, 2025Updated last year
- Recovery of eukaryotic genomes using contrastive learning. A specialized metagenomic binning tool designed for recovering high-quality eu…☆26Oct 6, 2026Updated last week
- An extensible and performant aligner and read mapper☆107Sep 15, 2026Updated 3 weeks ago
- Leviathan: Fast, memory-efficient, and scalable taxonomic and pathway profiling for (pan)genome-resolved metagenomics and metatranscripto…☆28Updated this week
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Meteor is a plateform for quantitative metagenomics profiling of complex ecosystems. Meteor relies on genes catalogue to perform species-…☆43Updated this week
- A package to annotate protein sequences☆63Feb 23, 2025Updated last year
- PanTax: Strain-level metagenomic profiling using pangenome graphs☆54Jun 10, 2026Updated 4 months ago
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆63May 5, 2026Updated 5 months ago
- 🐦 spideog - Command line utility for Kraken2 reports.☆11Nov 30, 2020Updated 5 years ago
- Fast tool to build the core genome of prokaryotic genomes. Can handle large datasets. Dependencis: Usearch & Numpy☆10Nov 26, 2025Updated 10 months ago
- GEne Cluster prediction with COnditional random fields.☆90Jul 29, 2026Updated 2 months ago
- Python bindings for the TaxonKit library☆43Oct 1, 2026Updated last week
- Convert genbank files to a swath of other formats☆32Aug 9, 2026Updated 2 months ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Nextflow pipeline for generation of phylogenetic trees to be visualized in Auspice.☆11Jan 6, 2026Updated 9 months ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and give confidences of microbial organisms within short- or long-read…☆83Updated this week
- TAXnomic Profile Aggregation and STAndardisation☆43May 2, 2026Updated 5 months ago
- ☆27Jun 20, 2023Updated 3 years ago
- Pipeline for identification of eukaryotic contigs in metagenomic assemblies☆14Mar 14, 2024Updated 2 years ago
- 🌟🧬 GraphBin-Tk: assembly graph-based metagenomic binning toolkit☆24Jun 25, 2026Updated 3 months ago
- The Microbial Co-occurrence Network Explorer☆21Oct 17, 2023Updated 2 years ago