metagenomics

There are 42 repositories under metagenomics topic.

MMseqs2
soedinglab / MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
bioinformatics sequence-clustering profile-search sequence-search linclust mmseqs metagenomics alignment blast taxonomy
Language:C 1346
torognes / vsearch
Versatile open-source tool for microbiome analysis
metabarcoding metagenomics chimera bioinformatics fastq fasta microbiome amplicon sequence-alignment clustering search
Language:C++ 652
voutcn / megahit
Ultra-fast and memory-efficient (meta-)genome assembler
bioinformatics metagenomics succinct data-structures genomics genome-assembly
Language:C++ 581
GTDBTk
Ecogenomics / GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
taxonomy species-assignments phylogenetics archaea bacteria nomenclature bioinformatics metagenomics
Language:Python 460
benjjneb / dada2
Accurate sample inference from amplicon data with single nucleotide resolution
amplicon bioconductor bioinformatics metabarcoding metagenomics microbiome taxonomy
Language:R 459
anvio
merenlab / anvio
An analysis and visualization platform for 'omics data
anvio bioinformatics comparative-genomics javascript metagenomics metatranscriptomics pangenomics phylogenomics population-genetics python science visualization
Language:Python 422
metagenome-atlas / atlas
ATLAS - Three commands to start analyzing your metagenome data
metagenomics annotation snakemake assembly genomic-binning functional-annotation taxonomic-classifications
Language:Python 364
jtamames / SqueezeMeta
A complete pipeline for metagenomic analysis
metagenomics pipeline metagenomes taxonomic-assignment
Language:C 356
training-material
galaxyproject / training-material
A collection of Galaxy-related training material
usegalaxy training materials ngs tutorial metagenomics proteomics rnaseq chip-seq hacktoberfest
Language:HTML 302
biobakery / MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
public tools biobakery python metagenomics
Language:Python 287
bioinformatics-centre / kaiju
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
metagenomics next-generation-sequencing bioinformatics taxonomic-classification taxonomy
Language:C 258
MrOlm / drep
Rapid comparison and dereplication of genomes
bioinformatics metagenomics microbiology assembly microbial-genomes
Language:Python 244
WrightonLabCSU / DRAM
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
bioinformatics genomics metagenome-assembled-genomes metagenomics viral-genomics viral-metagenomics annotation microbiome
Language:Python 241
fbreitwieser / krakenuniq
🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
bioinformatics metagenomics
Language:C++ 218
ropensci / biomartr
Genomic Data Retrieval with R
r genome-retrieval biomart database-retrieval ncbi-genbank genomics ensembl-servers sequenced-genomes proteome genome genome-annotation metagenomics meta-analysis rstats r-package peer-reviewed
Language:R 212
nf-core / mag
Assembly and binning of metagenomes
workflow nextflow metagenomics assembly binning annotation nf-core pipeline bioinformatics nanopore nanopore-sequencing metagenomes long-read-sequencing
Language:Nextflow 199
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
metagenomics computational-biology metabolic-models gut-microbiome snakemake metagenome-assembled-genomes mags metabolism bioinformatics flux-balance-analysis genome-scale-metabolic-model metabolic-modeling microbial-ecology microbiome systems-biology
Language:Python 186
HadrienG / InSilicoSeq
:rocket: A sequencing simulator
bioinformatics illumina-sequencing sequencing simulation metagenomics
Language:Python 178
kmcp
shenwei356 / kmcp
Accurate metagenomic profiling && Fast large-scale sequence/genome searching
kmer sketch searching metagenomics taxonomic-classification taxonomic-profiling scaled-minhash syncmers cobs sketching bigsi fracminhash virome
Language:Go 178
soedinglab / metaeuk
MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
metagenomics eukaryotes gene-prediction gene-discovery bioinformatics
Language:C 174
nf-core / ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
amplicon-sequencing 16s nf-core nextflow pipeline workflow metagenomics rrna 18s its metabarcoding qiime2 edna taxonomic-classification illumina iontorrent microbiome pacbio taxonomic-profiling
Language:Nextflow 171
yiluheihei / microbiomeMarker
R package for microbiome biomarker discovery
microbiome biomarker-discovery lefse metagenomics r differential-abundance-analysis r-package
Language:R 169
CAMI-challenge / CAMISIM
CAMISIM: Simulating metagenomes and microbial communities
metagenomics simulation
Language:Python 167
sunbeam-labs / sunbeam
A robust, extensible metagenomics pipeline
metagenomics snakemake reproducible-research
Language:Python 166
dnbaker / dashing
Fast and accurate genomic distances using HyperLogLog
sketch-data-structures metagenomics indexing hyperloglog
Language:C++ 160
bluenote-1577 / skani
Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.
average-nucleotide-identity bioinformatics metagenomics rust
Language:Rust 159
benjjneb / decontam
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
amplicon bioinformatics contamination metabarcoding metagenomics microbiome
Language:R 143
ngless-toolkit / ngless
NGLess: NGS with less work
haskell bioinformatics bioinformatics-pipeline samtools bwa next-generation-sequencing fastq-format fastq science ngs metagenomics genomics haskell-language
Language:Haskell 142
plass
soedinglab / plass
sensitive and precise assembly of short sequencing reads
bioinformatics metagenomics sequence-assembler proteins opensource proteomics metatranscriptomics
Language:C 140
nf-core / eager
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
nextflow ancientdna adna pipeline pathogen-genomics population-genetics nf-core workflow metagenomics bioinformatics genome ancient-dna-analysis
Language:Nextflow 134
bluenote-1577 / sylph
ultrafast genome querying and taxonomic profiling for metagenomic samples by abundance-corrected minhash.
average-nucleotide-identity k-mer metagenomics sketching-algorithm taxonomic-classification
Language:Rust 130
DNAnalyzer
VerisimilitudeX / DNAnalyzer
Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools.
amino-acid-sequence bioinformatics dna-sequencing regulatory-elements transcriptomics protein-sequences genomics sequencing metagenomics dna artificial-intelligence machine-learning
Language:Java 129
spacegraphcats / spacegraphcats
Indexing & querying large assembly graphs -- in space, no one can hear you miao!
bioinformatics k-mers metagenomics
Language:Standard ML 116
nf-core / viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
viral metagenomics amplicon assembly variant-calling illumina pipeline workflow nextflow nf-core covid-19 covid19 virus sars-cov-2 nanopore ont artic long-read-sequencing oxford-nanopore
Language:Nextflow 113
biobakery / Maaslin2
MaAsLin2: Microbiome Multivariate Association with Linear Models
biobakery bioconductor differential-abundance-analysis false-discovery-rate metagenomics microbiome multiple-covariates public repeated-measures tools
Language:R 112
ayixon / RaPDTool
Rapid Profiling and Deconvolution Tool for Metagenomes
bioinformatics metagenomics metagenome-assembled-genomes microbial-taxonomy
Language:Python 111