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The Top 23 Bioinformatics Microbiome Open Source Projects

Open source projects categorized as Bioinformatics Microbiome
Categories > Data Processing > Bioinformatics
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
Pandora ⭐ 127
PANDORA Advanced Machine Learning for Data Integration, Analysis, and Insightful Discoveries in Health and Disease 💻
most recent commit 6 months ago
Decontam ⭐ 122
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
most recent commit a year ago
Swarm ⭐ 110
A robust and fast clustering method for amplicon-based studies
most recent commit 3 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
Deepmicrobes ⭐ 61
DeepMicrobes: taxonomic classification for metagenomics with deep learning
most recent commit 2 years ago
Woltka ⭐ 58
Woltka: a versatile meta'omic data classifier
total releases 4most recent commit 4 months ago
Emperor ⭐ 52
Emperor a tool for the analysis and visualization of large microbial ecology datasets
total releases 34most recent commit 9 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
Redbiom ⭐ 42
Sample search by metadata and features
dependent packages 1total releases 10most recent commit 8 months agopypi redbiom} Downloads
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
Rdptools ⭐ 36
Collection of commonly used RDP Tools for easy building
most recent commit 3 years ago
Empress ⭐ 33
A fast and scalable phylogenetic tree viewer for microbiome data analysis
total releases 5most recent commit 2 years ago
Mmlong2 ⭐ 26
An all-in-one genome-centric metagenomics workflow using long reads
most recent commit 6 months ago
Qurro ⭐ 23
Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples
most recent commit a year ago
Ghost Tree ⭐ 23
creating hybrid-gene phylogenetic trees for diversity analyses
most recent commit 2 years ago
Calour ⭐ 23
exploratory and interactive microbiome analyses based on heatmaps
most recent commit a year ago
Mitre ⭐ 22
The Microbiome Interpretable Temporal Rule Engine
most recent commit 4 years ago
The 10 Latest Releases In Bioinformatics Microbiome Open Source Projects
Woltka ⭐ 58
Woltka: a versatile meta'omic data classifier
total releases 4latest release December 26, 2022most recent commit 4 months ago
Redbiom ⭐ 42
Sample search by metadata and features
dependent packages 1total releases 10latest release December 20, 2022most recent commit 8 months agopypi redbiom} Downloads
Qupid ⭐ 7
Case-control matching for microbiome data
total releases 3latest release June 23, 2022most recent commit 2 years ago
Xebec ⭐ 5
Snakemake pipeline for microbiome diversity effect size benchmarking
total releases 2latest release June 08, 2022most recent commit a year 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
Focus ⭐ 5
FOCUS: An Agile Profiler for Metagenomic Data
total releases 5latest release December 28, 2021most recent commit 2 years ago
Empress ⭐ 33
A fast and scalable phylogenetic tree viewer for microbiome data analysis
total releases 5latest release July 21, 2021most recent commit 2 years ago
Emperor ⭐ 52
Emperor a tool for the analysis and visualization of large microbial ecology datasets
total releases 34latest release April 15, 2021most recent commit 9 months ago
Vsearch ⭐ 605
Versatile open-source tool for microbiome analysis
total releases 1latest release March 03, 2021most recent commit 3 months ago
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