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The Top 23 Metagenomics Open Source Projects

Open source projects categorized as Metagenomics
Categories > Metagenomics
Mmseqs2 ⭐ 1,235
MMseqs2: ultra fast and sensitive search and clustering suite
most recent commit 2 months ago
Vsearch ⭐ 605
Versatile open-source tool for microbiome analysis
total releases 1most recent commit 3 months ago
Megahit ⭐ 442
Ultra-fast and memory-efficient (meta-)genome assembler
most recent commit a year ago
Dada2 ⭐ 428
Accurate sample inference from amplicon data with single nucleotide resolution
most recent commit 3 months ago
Anvio ⭐ 396
An analysis and visualization platform for 'omics data
most recent commit 3 months ago
Gtdbtk ⭐ 383
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
dependent packages 1total releases 48most recent commit 5 months agopypi gtdbtk} Downloads
Atlas ⭐ 332
ATLAS - Three commands to start analyzing your metagenome data
total releases 25most recent commit 3 months ago
Pavian ⭐ 328
🌈 Interactive analysis of metagenomics data
most recent commit 5 months ago
Squeezemeta ⭐ 308
A complete pipeline for metagenomic analysis
total releases 2most recent commit 4 months ago
Training Material ⭐ 284
A collection of Galaxy-related training material
most recent commit 3 months ago
Metaphlan ⭐ 242
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
dependent packages 1total releases 24most recent commit 4 months agopypi MetaPhlAn} Downloads
Kaiju ⭐ 236
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
most recent commit 5 months ago
Dram ⭐ 214
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
total releases 28most recent commit 3 months ago
Krakenuniq ⭐ 201
🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
most recent commit 3 months ago
Drep ⭐ 199
Rapid comparison and dereplication of genomes
dependent packages 1total releases 63most recent commit 7 months agopypi drep} Downloads
Biomartr ⭐ 198
Genomic Data Retrieval with R
dependent packages 3total releases 21most recent commit 5 months ago
Mag ⭐ 164
Assembly and binning of metagenomes
most recent commit 3 months ago
Kmcp ⭐ 161
Accurate metagenomic profiling && Fast large-scale sequence/genome searching
total releases 19most recent commit 7 months ago
Insilicoseq ⭐ 158
🚀 A sequencing simulator
dependent packages 1total releases 37most recent commit 4 months agopypi InSilicoSeq} Downloads
Sunbeam ⭐ 157
A robust, extensible metagenomics pipeline
most recent commit 3 months ago
Metagem ⭐ 155
💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
most recent commit 4 months ago
Microbiomemarker ⭐ 151
R package for microbiome biomarker discovery
most recent commit 6 months ago
Dashing ⭐ 147
Fast and accurate genomic distances using HyperLogLog
most recent commit a year ago
The 6 Most Depended On Metagenomics Open Source Projects
Biomartr ⭐ 198
Genomic Data Retrieval with R
dependent packages 3total releases 21latest release December 02, 2023most recent commit 5 months ago
Insilicoseq ⭐ 158
:rocket: A sequencing simulator
dependent packages 1total releases 37latest release August 10, 2023most recent commit 4 months agopypi InSilicoSeq} Downloads
Metaphlan ⭐ 242
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
dependent packages 1total releases 24latest release January 17, 2023most recent commit 4 months agopypi MetaPhlAn} Downloads
Gtdbtk ⭐ 383
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
dependent packages 1total releases 48latest release July 11, 2022most recent commit 5 months agopypi gtdbtk} Downloads
Drep ⭐ 199
Rapid comparison and dereplication of genomes
dependent packages 1total releases 63latest release September 15, 2023most recent commit 7 months agopypi drep} Downloads
Toolchest Client Python ⭐ 13
Toolchest Python client
dependent packages 1total releases 84latest release January 26, 2023most recent commit a year agopypi toolchest-client} Downloads
The 10 Latest Releases In Metagenomics Open Source Projects
Biomartr ⭐ 198
Genomic Data Retrieval with R
dependent packages 3total releases 21latest release December 02, 2023most recent commit 5 months ago
Gecco ⭐ 45
GEne Cluster prediction with COnditional random fields.
total releases 29latest release November 23, 2023most recent commit 5 months ago
Aviary ⭐ 62
A hybrid assembly and MAG recovery pipeline (and more!)
total releases 19latest release November 20, 2023most recent commit 3 months ago
Cosmosid Cli ⭐ 9
Command line client and Python libraries for CosmosID API
total releases 21latest release November 15, 2023most recent commit 5 months ago
Ggpicrust2 ⭐ 59
Make Picrust2 Output Analysis and Visualization Easier
total releases 10latest release November 08, 2023most recent commit 3 months ago
Semibin ⭐ 89
SemiBin: metagenomics binning with self-supervised deep learning
total releases 21latest release October 31, 2023most recent commit 3 months ago
Phables ⭐ 56
🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
total releases 17latest release October 09, 2023most recent commit 3 months ago
Kmcp ⭐ 161
Accurate metagenomic profiling && Fast large-scale sequence/genome searching
total releases 19latest release September 18, 2023most recent commit 7 months ago
Squeezemeta ⭐ 308
A complete pipeline for metagenomic analysis
total releases 2latest release September 18, 2023most recent commit 4 months ago
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