There are 42 repositories under metagenomics topic.
MMseqs2: ultra fast and sensitive search and clustering suite
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
ATLAS - Three commands to start analyzing your metagenome data
A complete pipeline for metagenomic analysis
A collection of Galaxy-related training material
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
:rocket: A sequencing simulator
Accurate metagenomic profiling && Fast large-scale sequence/genome searching
MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
R package for microbiome biomarker discovery
CAMISIM: Simulating metagenomes and microbial communities
A robust, extensible metagenomics pipeline
Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
NGLess: NGS with less work
sensitive and precise assembly of short sequencing reads
ultrafast genome querying and taxonomic profiling for metagenomic samples by abundance-corrected minhash.
Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools.
Indexing & querying large assembly graphs -- in space, no one can hear you miao!
Assembly and intrahost/low-frequency variant calling for viral samples