Topic: "metagenomics"
soedinglab/MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
Language: C - Size: 30.6 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 1,671 - Forks: 225
torognes/vsearch
Versatile open-source tool for microbiome analysis
Language: C++ - Size: 6.71 MB - Last synced at: 6 days ago - Pushed at: about 1 month ago - Stars: 700 - Forks: 127
voutcn/megahit
Ultra-fast and memory-efficient (meta-)genome assembler
Language: C++ - Size: 3.05 MB - Last synced at: 27 days ago - Pushed at: about 1 year ago - Stars: 650 - Forks: 138
Ecogenomics/GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Language: Python - Size: 28.8 MB - Last synced at: about 21 hours ago - Pushed at: about 1 month ago - Stars: 524 - Forks: 85
benjjneb/dada2
Accurate sample inference from amplicon data with single nucleotide resolution
Language: R - Size: 468 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 495 - Forks: 148
merenlab/anvio
An analysis and visualization platform for 'omics data
Language: Python - Size: 745 MB - Last synced at: about 22 hours ago - Pushed at: about 24 hours ago - Stars: 471 - Forks: 148
jtamames/SqueezeMeta
A complete pipeline for metagenomic analysis
Language: Scilab - Size: 695 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 416 - Forks: 84
metagenome-atlas/atlas
ATLAS - Three commands to start analyzing your metagenome data
Language: Python - Size: 20.3 MB - Last synced at: 7 days ago - Pushed at: 27 days ago - Stars: 390 - Forks: 100
biobakery/MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
Language: Python - Size: 7.51 MB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 340 - Forks: 89
galaxyproject/training-material
A collection of Galaxy-related training material
Language: HTML - Size: 26.2 GB - Last synced at: about 1 hour ago - Pushed at: about 2 hours ago - Stars: 331 - Forks: 971
MrOlm/drep
Rapid comparison and dereplication of genomes
Language: Python - Size: 16.5 MB - Last synced at: 14 days ago - Pushed at: about 2 months ago - Stars: 290 - Forks: 38
WrightonLabCSU/DRAM
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
Language: Python - Size: 14.6 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 279 - Forks: 55
bioinformatics-centre/kaiju
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
Language: C - Size: 906 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 278 - Forks: 67
nf-core/mag
Assembly and binning of metagenomes
Language: Nextflow - Size: 36.5 MB - Last synced at: about 15 hours ago - Pushed at: about 21 hours ago - Stars: 238 - Forks: 131
fbreitwieser/krakenuniq
🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
Language: C++ - Size: 1.88 MB - Last synced at: 4 days ago - Pushed at: over 1 year ago - Stars: 232 - Forks: 43
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
Language: Python - Size: 262 MB - Last synced at: about 2 months ago - Pushed at: 10 months ago - Stars: 231 - Forks: 47
bluenote-1577/sylph
ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
Language: Rust - Size: 27.6 MB - Last synced at: 12 days ago - Pushed at: 3 months ago - Stars: 229 - Forks: 9
ropensci/biomartr
Genomic Data Retrieval with R
Language: R - Size: 5.86 MB - Last synced at: 7 days ago - Pushed at: 4 months ago - Stars: 222 - Forks: 29
nf-core/ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Language: Nextflow - Size: 16.6 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 203 - Forks: 136
HadrienG/InSilicoSeq
:rocket: A sequencing simulator
Language: Python - Size: 9.44 MB - Last synced at: 29 days ago - Pushed at: 2 months ago - Stars: 197 - Forks: 36
bluenote-1577/skani
Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.
Language: Rust - Size: 42.7 MB - Last synced at: 10 days ago - Pushed at: 11 months ago - Stars: 197 - Forks: 13
shenwei356/kmcp
Accurate metagenomic profiling && Fast large-scale sequence/genome searching
Language: Go - Size: 82.1 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 187 - Forks: 13
soedinglab/metaeuk
MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
Language: C - Size: 14.1 MB - Last synced at: 2 months ago - Pushed at: 11 months ago - Stars: 183 - Forks: 23
yiluheihei/microbiomeMarker
R package for microbiome biomarker discovery
Language: R - Size: 23.7 MB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 177 - Forks: 41
sunbeam-labs/sunbeam
A robust, extensible metagenomics pipeline
Language: Python - Size: 21 MB - Last synced at: 5 days ago - Pushed at: 6 days ago - Stars: 170 - Forks: 43
nf-core/eager
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Language: Nextflow - Size: 64 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 169 - Forks: 83
CAMI-challenge/CAMISIM
CAMISIM: Simulating metagenomes and microbial communities
Language: Python - Size: 430 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 162 - Forks: 36
dnbaker/dashing
Fast and accurate genomic distances using HyperLogLog
Language: C++ - Size: 877 MB - Last synced at: 2 months ago - Pushed at: over 2 years ago - Stars: 160 - Forks: 12
benjjneb/decontam
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
Language: R - Size: 1.25 MB - Last synced at: 21 days ago - Pushed at: about 2 years ago - Stars: 157 - Forks: 27
soedinglab/plass
sensitive and precise assembly of short sequencing reads
Language: C - Size: 27.1 MB - Last synced at: 10 days ago - Pushed at: 8 months ago - Stars: 155 - Forks: 15
nf-core/taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Language: Nextflow - Size: 16 MB - Last synced at: 1 day ago - Pushed at: 2 days ago - Stars: 148 - Forks: 51
ngless-toolkit/ngless
NGLess: NGS with less work
Language: Haskell - Size: 14.1 MB - Last synced at: 13 days ago - Pushed at: 3 months ago - Stars: 146 - Forks: 25
wwood/singlem
Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes
Language: Python - Size: 303 MB - Last synced at: 13 days ago - Pushed at: 17 days ago - Stars: 142 - Forks: 18
steineggerlab/Metabuli
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
Language: C++ - Size: 92.4 MB - Last synced at: 11 days ago - Pushed at: 13 days ago - Stars: 139 - Forks: 12
biobakery/Maaslin2
MaAsLin2: Microbiome Multivariate Association with Linear Models
Language: R - Size: 1.19 MB - Last synced at: 19 days ago - Pushed at: 7 months ago - Stars: 138 - Forks: 35
nf-core/viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
Language: Nextflow - Size: 9.89 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 137 - Forks: 128
cafferychen777/ggpicrust2
Make Picrust2 Output Analysis and Visualization Easier
Language: R - Size: 23.9 MB - Last synced at: 12 days ago - Pushed at: 15 days ago - Stars: 134 - Forks: 20
BigDataBiology/SemiBin
SemiBin: metagenomics binning with self-supervised deep learning
Language: Python - Size: 106 MB - Last synced at: 3 days ago - Pushed at: 3 months ago - Stars: 134 - Forks: 12
eric9n/Kun-peng
Kun-peng: an ultra-fast, low-memory footprint and accurate taxonomy classifier for all
Language: Rust - Size: 3.12 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 124 - Forks: 11
ratschlab/metagraph
Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly
Language: C++ - Size: 74.8 MB - Last synced at: 1 day ago - Pushed at: 2 days ago - Stars: 119 - Forks: 17
spacegraphcats/spacegraphcats
Indexing & querying large assembly graphs -- in space, no one can hear you miao!
Language: Standard ML - Size: 40.5 MB - Last synced at: 24 days ago - Pushed at: over 1 year ago - Stars: 117 - Forks: 15
microsud/Tools-Microbiome-Analysis
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
Language: CSS - Size: 6.07 MB - Last synced at: 7 days ago - Pushed at: about 2 years ago - Stars: 115 - Forks: 46
ayixon/RaPDTool
Rapid Profiling and Deconvolution Tool for Metagenomes
Language: Python - Size: 7.98 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 111 - Forks: 87
grimmlab/MicrobiomeBestPracticeReview
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
Language: Shell - Size: 13 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 101 - Forks: 36
louiejtaylor/grabseqs
A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA
Language: Python - Size: 281 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 101 - Forks: 15
rhysnewell/aviary
A hybrid assembly and MAG recovery pipeline (and more!)
Language: Python - Size: 38.8 MB - Last synced at: 12 days ago - Pushed at: 13 days ago - Stars: 96 - Forks: 15
pirovc/ganon
ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
Language: Python - Size: 24.2 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 96 - Forks: 12
khyox/recentrifuge
Recentrifuge: robust comparative analysis and contamination removal for metagenomics
Language: Python - Size: 14.1 MB - Last synced at: 12 days ago - Pushed at: about 1 month ago - Stars: 94 - Forks: 8
metagentools/GraphBin
✨🧬 Refined binning of metagenomic contigs using assembly graphs
Language: Python - Size: 54.3 MB - Last synced at: 9 days ago - Pushed at: 3 months ago - Stars: 92 - Forks: 7
nf-core/funcscan
(Meta-)genome screening for functional and natural product gene sequences
Language: Nextflow - Size: 24.5 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 87 - Forks: 23
jolespin/veba
A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
Language: Python - Size: 55 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 84 - Forks: 11
meringlab/FlashWeave.jl
Inference of microbial interaction networks from large-scale heterogeneous abundance data
Language: Julia - Size: 1.31 MB - Last synced at: 6 days ago - Pushed at: 12 months ago - Stars: 84 - Forks: 8
broadinstitute/catch
A package for designing compact and comprehensive capture probe sets.
Language: Python - Size: 5.68 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 83 - Forks: 16
katerinakazantseva/strainy
Graph-based assembly phasing
Language: Python - Size: 17.2 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 80 - Forks: 6
BigDataBiology/macrel
Predict AMPs in (meta)genomes and peptides
Language: Python - Size: 63.6 MB - Last synced at: 2 days ago - Pushed at: 4 months ago - Stars: 79 - Forks: 13
seqan/lambda
LAMBDA – the Local Aligner for Massive Biological DatA
Language: C++ - Size: 2.28 MB - Last synced at: 18 days ago - Pushed at: 9 months ago - Stars: 79 - Forks: 20
Vini2/phables
🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
Language: Python - Size: 7.29 MB - Last synced at: 2 days ago - Pushed at: 8 months ago - Stars: 77 - Forks: 5
qiyunzhu/woltka
Woltka: a versatile meta'omic data classifier
Language: Python - Size: 20 MB - Last synced at: 12 days ago - Pushed at: 2 months ago - Stars: 74 - Forks: 25
MicrobeLab/DeepMicrobes
DeepMicrobes: taxonomic classification for metagenomics with deep learning
Language: Python - Size: 1.25 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 74 - Forks: 19
SPAAM-community/AncientMetagenomeDir
Repository containing lists of all published ancient metagenomic (and related) samples and libraries
Language: HTML - Size: 165 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 72 - Forks: 33
linxingchen/cobra
A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.
Language: Python - Size: 332 KB - Last synced at: 17 days ago - Pushed at: 10 months ago - Stars: 70 - Forks: 11
dnbaker/bonsai
Bonsai: Fast, flexible taxonomic analysis and classification
Language: C++ - Size: 74.1 MB - Last synced at: 2 months ago - Pushed at: about 1 year ago - Stars: 70 - Forks: 10
zellerlab/GECCO
GEne Cluster prediction with COnditional random fields.
Language: Python - Size: 28.8 MB - Last synced at: 9 days ago - Pushed at: 2 months ago - Stars: 67 - Forks: 8
StevenWingett/FastQ-Screen
Detecting contamination in NGS data and multi-species analysis
Language: HTML - Size: 1.97 MB - Last synced at: 6 months ago - Pushed at: 7 months ago - Stars: 67 - Forks: 16
will-rowe/groot
A resistome profiler for Graphing Resistance Out Of meTagenomes
Language: Go - Size: 12.5 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 61 - Forks: 6
muellan/metacache
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
Language: C++ - Size: 149 MB - Last synced at: 16 days ago - Pushed at: 2 months ago - Stars: 60 - Forks: 13
Kalan-Lab/zol
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
Language: Python - Size: 83.3 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 59 - Forks: 4
ibe-uw/tiara
tiara – a tool for DNA sequence classification
Language: Python - Size: 105 MB - Last synced at: 20 days ago - Pushed at: over 1 year ago - Stars: 59 - Forks: 10
songweizhi/MetaCHIP
Horizontal gene transfer (HGT) identification pipeline
Language: Python - Size: 227 MB - Last synced at: 21 days ago - Pushed at: about 2 years ago - Stars: 58 - Forks: 16
cmkobel/CompareM2
🦠📇 Microbial genomes-to-report pipeline
Language: Python - Size: 95.6 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 56 - Forks: 3
iquasere/KEGGCharter
A tool for representing genomic potential and transcriptomic expression into KEGG pathways
Language: Python - Size: 519 MB - Last synced at: about 2 months ago - Pushed at: 10 months ago - Stars: 54 - Forks: 7
smdabdoub/kraken-biom
Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
Language: Python - Size: 43.9 KB - Last synced at: 5 days ago - Pushed at: about 3 years ago - Stars: 54 - Forks: 17
xinehc/args_oap
ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database
Language: Python - Size: 87.3 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 52 - Forks: 12
leylabmpi/Struo2
Scalable creating/updating of metagenome profiling databases
Language: Jupyter Notebook - Size: 12.8 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 49 - Forks: 7
Russel88/DAtest
Compare different differential abundance and expression methods
Language: R - Size: 1.54 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 46 - Forks: 9
Serka-M/mmlong2
Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes
Language: Python - Size: 2.71 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 45 - Forks: 5
SegataLab/panphlan
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
Language: Python - Size: 292 KB - Last synced at: 23 days ago - Pushed at: over 1 year ago - Stars: 45 - Forks: 6
Arkadiy-Garber/FeGenie
HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes
Language: Python - Size: 99.3 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 44 - Forks: 10
JensUweUlrich/Taxor
Fast and space-efficient taxonomic classification of long reads
Language: C++ - Size: 716 KB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 43 - Forks: 2
dib-lab/charcoal
Remove contaminated contigs from genomes using k-mers and taxonomies.
Language: Python - Size: 19.4 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 43 - Forks: 1
MG-RAST/MG-RAST
The MG-RAST Backend -- the API server
Language: Perl - Size: 15.7 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 43 - Forks: 27
leylabmpi/Struo
Ley Lab MetaGenome Profiler DataBase generator
Language: Jupyter Notebook - Size: 9.56 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 43 - Forks: 3
lmrodriguezr/nonpareil
Estimate metagenomic coverage and sequence diversity
Language: C++ - Size: 15.8 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 42 - Forks: 11
metagentools/MetaCoAG
🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs
Language: Python - Size: 156 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 42 - Forks: 3
KwanLab/Autometa
Autometa: Automated Extraction of Genomes from Shotgun Metagenomes
Language: Python - Size: 78.9 MB - Last synced at: about 2 months ago - Pushed at: 4 months ago - Stars: 41 - Forks: 15
hzi-bifo/traitar Fork of aweimann/traitar
From genomes to phenotypes: Traitar, the microbial trait analyzer
Language: Python - Size: 31.3 MB - Last synced at: over 2 years ago - Pushed at: almost 6 years ago - Stars: 41 - Forks: 15
liaoherui/StrainScan
High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers
Language: Python - Size: 56.7 MB - Last synced at: 15 days ago - Pushed at: about 1 year ago - Stars: 40 - Forks: 6
taxprofiler/taxpasta
TAXnomic Profile Aggregation and STAndardisation
Language: Python - Size: 1.98 MB - Last synced at: 11 days ago - Pushed at: 7 months ago - Stars: 39 - Forks: 8
MHH-RCUG/Wochenende
Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3
Language: Python - Size: 40.7 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 37 - Forks: 16
shandley/awesome-virome
A listing of software, tools and databases useful for virome analysis
Language: HTML - Size: 50.4 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 36 - Forks: 7
Arcadia-Science/metagenomics
A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies
Language: Nextflow - Size: 2.41 MB - Last synced at: about 2 months ago - Pushed at: about 2 years ago - Stars: 36 - Forks: 3
jhuapl-bio/taxtriage
TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various use-cases of mNGS in mind.
Language: Python - Size: 115 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 35 - Forks: 5
iquasere/MOSCA
Meta-Omics Software for Community Analysis
Language: Python - Size: 441 MB - Last synced at: about 2 months ago - Pushed at: 7 months ago - Stars: 35 - Forks: 4
biobakery/melonnpan
Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
Language: R - Size: 3.81 MB - Last synced at: about 2 months ago - Pushed at: about 1 year ago - Stars: 35 - Forks: 8
LottePronk/whokaryote
Classify metagenomic contigs as eukaryotic or prokaryotic
Language: Python - Size: 8.29 MB - Last synced at: 7 days ago - Pushed at: over 2 years ago - Stars: 35 - Forks: 7
genotoul-bioinfo/Binette
A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.
Language: Python - Size: 591 KB - Last synced at: 4 days ago - Pushed at: 10 days ago - Stars: 34 - Forks: 1
prophyle/prophyle
Accurate, resource-frugal and deterministic DNA sequence classifier.
Language: Python - Size: 30.3 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 34 - Forks: 5
xinehc/melon
Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
Language: Python - Size: 47.9 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 34 - Forks: 1
metagentools/GraphBin2
☯️🧬 Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs
Language: Python - Size: 89.4 MB - Last synced at: 20 days ago - Pushed at: 3 months ago - Stars: 34 - Forks: 3
microsud/microbiomeutilities
The is mostly a wrapper tool using phyloseq and microbiome R packages.
Language: R - Size: 40 MB - Last synced at: 20 days ago - Pushed at: over 2 years ago - Stars: 34 - Forks: 7