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The Top 23 Python Metagenomics Open Source Projects

Open source projects categorized as Python Metagenomics
Categories > Metagenomics
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
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
Drep ⭐ 199
Rapid comparison and dereplication of genomes
dependent packages 1total releases 63most recent commit 7 months agopypi drep} Downloads
Insilicoseq ⭐ 158
🚀 A sequencing simulator
dependent packages 1total releases 37most recent commit 4 months agopypi InSilicoSeq} Downloads
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
Camisim ⭐ 115
CAMISIM: Simulating metagenomes and microbial communities
most recent commit 10 months ago
Rapdtool ⭐ 110
Rapid Profiling and Deconvolution Tool for Metagenomes
most recent commit 3 months ago
Semibin ⭐ 89
SemiBin: metagenomics binning with self-supervised deep learning
total releases 21most recent commit 3 months ago
Recentrifuge ⭐ 83
Recentrifuge: robust comparative analysis and contamination removal for metagenomics
total releases 77most recent commit 3 months ago
Graphbin ⭐ 80
✨🧬 Refined binning of metagenomic contigs using assembly graphs
total releases 4most recent commit 4 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
Metagenomics Index Correction ⭐ 67
most recent commit 7 months ago
Catch ⭐ 63
A package for designing compact and comprehensive capture probe sets.
most recent commit 6 months ago
Aviary ⭐ 62
A hybrid assembly and MAG recovery pipeline (and more!)
total releases 19most 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
Phables ⭐ 56
🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
total releases 17most recent commit 3 months ago
Macrel ⭐ 48
Predict AMPs in (meta)genomes and peptides
most recent commit 4 months ago
Metapi ⭐ 46
A general metagenomics data mining system focus on robust microbiome research
total releases 42most recent commit 6 months ago
Gecco ⭐ 45
GEne Cluster prediction with COnditional random fields.
total releases 29most recent commit 5 months ago
Grabseqs ⭐ 44
A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA
total releases 11most recent commit 4 years ago
The 5 Most Depended On Python Metagenomics Open Source Projects
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 Python Metagenomics Open Source Projects
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
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
Drep ⭐ 199
Rapid comparison and dereplication of genomes
dependent packages 1total releases 63latest release September 15, 2023most recent commit 7 months agopypi drep} Downloads
Pydamage ⭐ 7
Damage parameter estimation for ancient DNA
total releases 14latest release September 01, 2023most recent commit 8 months ago
Insilicoseq ⭐ 158
:rocket: A sequencing simulator
dependent packages 1total releases 37latest release August 10, 2023most recent commit 4 months agopypi InSilicoSeq} Downloads
Graphbin ⭐ 80
✨🧬 Refined binning of metagenomic contigs using assembly graphs
total releases 4latest release July 25, 2023most recent commit 4 months ago
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