Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
☆409Mar 2, 2026Updated last month
Alternatives and similar repositories for CheckM
Users that are interested in CheckM are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Assessing the quality of metagenome-derived genome bins using machine learning☆254Mar 20, 2025Updated last year
- GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.☆593Apr 21, 2026Updated last week
- Rapid comparison and dereplication of genomes☆336Nov 10, 2025Updated 5 months ago
- hybrid assembly pipeline for bacterial genomes☆639Jul 25, 2024Updated last year
- A toolbox for improving metagenome-assembled genomes.☆64Jun 2, 2021Updated 4 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Rapid prokaryotic genome annotation☆975Jan 6, 2026Updated 3 months ago
- Read alignment statistics for metagenomics☆396Apr 8, 2026Updated 3 weeks ago
- Fast Whole-Genome Similarity (ANI) Estimation☆454Dec 16, 2025Updated 4 months ago
- DAS Tool☆172May 2, 2024Updated last year
- MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis☆467Jul 28, 2023Updated 2 years ago
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆633Feb 18, 2026Updated 2 months ago
- Fast genome-wide functional annotation through orthology assignment☆730Mar 24, 2026Updated last month
- Prodigal Gene Prediction Software☆537Jan 23, 2024Updated 2 years ago
- Clustering cONtigs with COverage and ComposiTion☆137Mar 6, 2020Updated 6 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Metagenomic binning suite☆29Sep 30, 2022Updated 3 years ago
- Microbial RNA annotation☆290Apr 12, 2026Updated 2 weeks ago
- A tool to circularize genome assemblies☆254Apr 6, 2024Updated 2 years ago
- Bioinformatics program inStrain☆184Mar 12, 2026Updated last month
- A tool for generating consensus long-read assemblies for bacterial genomes☆342Sep 11, 2025Updated 7 months ago
- An updated pipeline for pangenome investigation☆356Apr 22, 2026Updated last week
- geNomad: Identification of mobile genetic elements☆303Mar 29, 2026Updated last month
- SPAdes Genome Assembler☆931Apr 13, 2026Updated 2 weeks ago
- MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data☆402Mar 16, 2026Updated last month
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Fast taxonomic classification of metagenomic sequencing reads using a protein reference database☆302Apr 25, 2025Updated last year
- Mass screening of contigs for antimicrobial and virulence genes☆491Apr 3, 2026Updated 3 weeks ago
- AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and p…☆359Mar 29, 2026Updated last month
- SemiBin: metagenomics binning with self-supervised deep learning☆159Updated this week
- Variational autoencoder for metagenomic binning☆322Updated this week
- ☆64Feb 27, 2024Updated 2 years ago
- CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metage…☆229Apr 1, 2026Updated 3 weeks ago
- Fast genome and metagenome distance estimation using MinHash☆440Sep 19, 2025Updated 7 months ago
- Application and Python module for average nucleotide identity analyses of microbes.☆216Jul 1, 2025Updated 9 months ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Rapid large-scale prokaryote pan genome analysis☆377Nov 3, 2025Updated 5 months ago
- A hybrid assembly and MAG recovery pipeline (and more!)☆106Updated this week
- 🌈 Interactive analysis of metagenomics data☆449Sep 17, 2025Updated 7 months ago
- customizable pipeline to identify viral sequences from (meta)genomic data☆288Nov 28, 2024Updated last year
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆249Oct 12, 2025Updated 6 months ago
- Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes☆332Apr 20, 2026Updated last week
- Classifier for metagenomic sequences☆274Apr 15, 2026Updated 2 weeks ago