Microbiome classification pipeline
☆67May 13, 2025Updated 11 months ago
Alternatives and similar repositories for CCMetagen
Users that are interested in CCMetagen are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆58Apr 8, 2026Updated 3 weeks ago
- A toolbox for improving metagenome-assembled genomes.☆64Jun 2, 2021Updated 4 years ago
- Scalable creating/updating of metagenome profiling databases☆62Jun 25, 2025Updated 10 months ago
- ☆15Oct 14, 2023Updated 2 years ago
- ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refse…☆104Apr 23, 2026Updated 2 weeks 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.
- Autometa: Automated Extraction of Genomes from Shotgun Metagenomes☆45Jan 24, 2025Updated last year
- Nanopore read de-multiplexer☆13Mar 25, 2020Updated 6 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 last month
- 🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs☆69Sep 26, 2024Updated last year
- ☆34Feb 10, 2025Updated last year
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆56Apr 29, 2026Updated last week
- Eukfinder: A pipeline to retrieve microbial eukaryote genomes from metagenomic sequencing data☆29Jan 15, 2026Updated 3 months ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Apr 1, 2023Updated 3 years ago
- Assessing the quality of metagenome-derived genome bins using machine learning☆257Mar 20, 2025Updated last year
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A hybrid assembly and MAG recovery pipeline (and more!)☆106Apr 29, 2026Updated last week
- Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!☆184Mar 17, 2026Updated last month
- Rapid comparison and dereplication of genomes☆336Nov 10, 2025Updated 5 months ago
- kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding☆23Aug 23, 2023Updated 2 years ago
- Read alignment statistics for metagenomics☆396Apr 8, 2026Updated 3 weeks ago
- Metaphor: a general-purpose workflow for assembly and binning of metagenomes☆40Nov 14, 2025Updated 5 months ago
- Short Read Sequence Typing for Bacterial Pathogens☆149Jun 20, 2021Updated 4 years ago
- Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.☆147Dec 17, 2025Updated 4 months ago
- DeepMicrobes: taxonomic classification for metagenomics with deep learning☆105Sep 17, 2022Updated 3 years ago
- 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.
- mLDM: a new hierarchical Bayesian statistical model for sparse microbial association discovery☆11Oct 18, 2016Updated 9 years ago
- ☆42Feb 14, 2021Updated 5 years ago
- Antimicrobial Resistance Identification By Assembly☆187Oct 12, 2023Updated 2 years ago
- A Python package for obtaining, parsing and exploring biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)☆50Apr 24, 2026Updated last week
- Fast and accurate set similarity estimation via containment min hash☆42Jul 19, 2024Updated last year
- Highly sensitive pathogen detection☆12Oct 5, 2020Updated 5 years ago
- customizable pipeline to identify viral sequences from (meta)genomic data☆289Nov 28, 2024Updated last year
- GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.☆597Apr 21, 2026Updated 2 weeks ago
- TAXnomic Profile Aggregation and STAndardisation☆43Updated this week
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- MAGScoT - a MAG scoring and refinement tool☆44Apr 8, 2026Updated 3 weeks ago
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆60Feb 7, 2026Updated 3 months ago
- MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs☆25Mar 19, 2023Updated 3 years ago
- viralComplete: BLAST-based viral completeness verification☆23Oct 4, 2021Updated 4 years ago
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆20Oct 8, 2025Updated 6 months ago
- 🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results☆245Jan 18, 2024Updated 2 years ago
- Assessing and Improving the quality of metagenomic assemblies☆31Feb 21, 2022Updated 4 years ago