metagenomics
There are 672 repositories under metagenomics topic.
soedinglab/MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
torognes/vsearch
Versatile open-source tool for microbiome analysis
voutcn/megahit
Ultra-fast and memory-efficient (meta-)genome assembler
Ecogenomics/GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
benjjneb/dada2
Accurate sample inference from amplicon data with single nucleotide resolution
merenlab/anvio
An analysis and visualization platform for 'omics data
jtamames/SqueezeMeta
A complete pipeline for metagenomic analysis
metagenome-atlas/atlas
ATLAS - Three commands to start analyzing your metagenome data
biobakery/MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
galaxyproject/training-material
A collection of Galaxy-related training material
bioinformatics-centre/kaiju
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
MrOlm/drep
Rapid comparison and dereplication of genomes
WrightonLabCSU/DRAM
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
fbreitwieser/krakenuniq
🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
nf-core/mag
Assembly and binning of metagenomes
ropensci/biomartr
Genomic Data Retrieval with R
franciscozorrilla/metaGEM
: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
bluenote-1577/sylph
ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
HadrienG/InSilicoSeq
:rocket: A sequencing simulator
nf-core/ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
CAMI-challenge/CAMISIM
CAMISIM: Simulating metagenomes and microbial communities
shenwei356/kmcp
Accurate metagenomic profiling && Fast large-scale sequence/genome searching
soedinglab/metaeuk
MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
bluenote-1577/skani
Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.
yiluheihei/microbiomeMarker
R package for microbiome biomarker discovery
sunbeam-labs/sunbeam
A robust, extensible metagenomics pipeline
dnbaker/dashing
Fast and accurate genomic distances using HyperLogLog
nf-core/eager
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
soedinglab/plass
sensitive and precise assembly of short sequencing reads
benjjneb/decontam
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
ngless-toolkit/ngless
NGLess: NGS with less work
nf-core/taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
nf-core/viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
biobakery/Maaslin2
MaAsLin2: Microbiome Multivariate Association with Linear Models
steineggerlab/Metabuli
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
BigDataBiology/SemiBin
SemiBin: metagenomics binning with self-supervised deep learning