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The Top 23 Bioinformatics Taxonomy Open Source Projects

Open source projects categorized as Bioinformatics Taxonomy
Categories > Data Processing > Bioinformatics
Categories > Taxonomy
Mmseqs2 ⭐ 1,235
MMseqs2: ultra fast and sensitive search and clustering suite
most recent commit 2 months ago
Dada2 ⭐ 428
Accurate sample inference from amplicon data with single nucleotide resolution
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
Taxonkit ⭐ 306
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
total releases 53most recent commit 5 months ago
Kaiju ⭐ 236
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
most recent commit 5 months ago
Pyani ⭐ 140
Application and Python module for average nucleotide identity analyses of microbes.
dependent packages 1total releases 18most recent commit 2 years agopypi pyani} Downloads
Bio ⭐ 86
A lightweight and high-performance bioinformatics package in Golang
dependent packages 13total releases 32most 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
Metabuli ⭐ 54
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
most recent commit 3 months ago
Metacache ⭐ 49
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
most recent commit a year ago
Aniclustermap ⭐ 38
A tool for drawing ANI clustermap between all-vs-all microbial genomes
total releases 5most recent commit 6 months ago
Kraken Biom ⭐ 33
Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
total releases 1most recent commit 2 years ago
Taxadb ⭐ 32
🐣 locally query the ncbi taxonomy
total releases 11most recent commit 2 years ago
Miga ⭐ 29
MiGA: Microbial Genomes Atlas
most recent commit 3 months ago
Gtdb Taxdump ⭐ 29
GTDB taxonomy taxdump files with trackable TaxIds
most recent commit 10 months ago
Multitax ⭐ 23
Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)
total releases 7most recent commit a year ago
Phantasm ⭐ 20
PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes
most recent commit 5 months ago
Whokaryote ⭐ 17
Classify metagenomic contigs as eukaryotic or prokaryotic
most recent commit a year ago
Pytaxonkit ⭐ 17
Python bindings for the TaxonKit library
most recent commit a year ago
Gtaxon ⭐ 15
gTaxon - a fast cross-platform NCBI taxonomy data querying (gi2taxid, taxid2taxon, name2taxid, LCA) tool, with cmd client and REST API server for both local and remote server.
total releases 1most recent commit 8 years ago
Pyfastani ⭐ 14
Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
total releases 9most recent commit 9 months ago
Pyskani ⭐ 13
PyO3 bindings and Python interface to skani, a method for fast fast genomic identity calculation using sparse chaining.
total releases 2most recent commit a year ago
Taxor ⭐ 13
Fast and space-efficient taxonomic classification of long reads
most recent commit 3 months ago
The 3 Most Depended On Bioinformatics Taxonomy Open Source Projects
Bio ⭐ 86
A lightweight and high-performance bioinformatics package in Golang
dependent packages 13total releases 32latest release November 11, 2023most recent commit 4 months ago
Pyani ⭐ 140
Application and Python module for average nucleotide identity analyses of microbes.
dependent packages 1total releases 18latest release July 27, 2022most recent commit 2 years agopypi pyani} 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
The 10 Latest Releases In Bioinformatics Taxonomy Open Source Projects
Bio ⭐ 86
A lightweight and high-performance bioinformatics package in Golang
dependent packages 13total releases 32latest release November 11, 2023most recent commit 4 months ago
Aniclustermap ⭐ 38
A tool for drawing ANI clustermap between all-vs-all microbial genomes
total releases 5latest release November 07, 2023most recent commit 6 months ago
Pyani ⭐ 140
Application and Python module for average nucleotide identity analyses of microbes.
dependent packages 1total releases 18latest release July 27, 2022most recent commit 2 years agopypi pyani} 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
Taxadb ⭐ 32
:hatching_chick: locally query the ncbi taxonomy
total releases 11latest release June 14, 2022most recent commit 2 years ago
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