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The Top 23 Metagenomics Microbiome Open Source Projects

Open source projects categorized as Metagenomics Microbiome
Categories > Metagenomics
Categories > Microbiome
Vsearch ⭐ 605
Versatile open-source tool for microbiome analysis
total releases 1most recent commit 3 months ago
Dada2 ⭐ 428
Accurate sample inference from amplicon data with single nucleotide resolution
most recent commit 3 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
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 5 months ago
Ampliseq ⭐ 141
Amplicon sequencing analysis workflow using DADA2 and QIIME2
most recent commit 3 months ago
Decontam ⭐ 122
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
most recent commit a year ago
Maaslin2 ⭐ 86
MaAsLin2: Microbiome Multivariate Association with Linear Models
most recent commit 7 months ago
Taxprofiler ⭐ 78
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
most recent commit 3 months ago
Ganon ⭐ 73
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
most recent commit 3 months ago
Ancientmetagenomedir ⭐ 61
Repository containing lists of all published ancient metagenomic (and related) samples and libraries
most recent commit 3 months ago
Deepmicrobes ⭐ 61
DeepMicrobes: taxonomic classification for metagenomics with deep learning
most recent commit 2 years ago
Ggpicrust2 ⭐ 59
Make Picrust2 Output Analysis and Visualization Easier
total releases 10most recent commit 3 months ago
Woltka ⭐ 58
Woltka: a versatile meta'omic data classifier
total releases 4most recent commit 4 months ago
Flashweave.jl ⭐ 52
Inference of microbial interaction networks from large-scale heterogeneous abundance data
most recent commit 10 months ago
Microbiomebestpracticereview ⭐ 45
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
most recent commit 2 years ago
Panphlan ⭐ 38
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
total releases 2most recent commit 7 months ago
Datest ⭐ 34
Compare different differential abundance and expression methods
most recent commit 2 years ago
Microbiomeutilities ⭐ 29
The is mostly a wrapper tool using phyloseq and microbiome R packages.
most recent commit a year ago
Mmlong2 ⭐ 26
An all-in-one genome-centric metagenomics workflow using long reads
most recent commit 6 months ago
Melonnpan ⭐ 24
Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
most recent commit a year ago
Tweedieverse ⭐ 24
Differential analysis of multi-omics data based on the Tweedie distribution
most recent commit 4 months ago
Stag Mwc ⭐ 24
StaG Metagenomic Workflow Collaboration
most recent commit 3 months ago
The 7 Latest Releases In Metagenomics Microbiome Open Source Projects
Ggpicrust2 ⭐ 59
Make Picrust2 Output Analysis and Visualization Easier
total releases 10latest release November 08, 2023most recent commit 3 months ago
Woltka ⭐ 58
Woltka: a versatile meta'omic data classifier
total releases 4latest release December 26, 2022most recent commit 4 months ago
Super Focus ⭐ 19
A tool for agile functional analysis of shotgun metagenomic data
total releases 10latest release April 11, 2022most recent commit 3 months ago
Vsearch ⭐ 605
Versatile open-source tool for microbiome analysis
total releases 1latest release March 03, 2021most recent commit 3 months ago
Famli ⭐ 8
Functional Analysis of Metagenomes by Likelihood Inference
total releases 3latest release February 23, 2020most recent commit 4 years ago
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