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26 search results found

Mmseqs2 ⭐ 1,235

MMseqs2: ultra fast and sensitive search and clustering suite

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Accurate sample inference from amplicon data with single nucleotide resolution

Taxonkit ⭐ 306

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Application and Python module for average nucleotide identity analyses of microbes.

A lightweight and high-performance bioinformatics package in Golang

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

Metabuli ⭐ 54

Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

Metacache ⭐ 49

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

Aniclustermap ⭐ 38

A tool for drawing ANI clustermap between all-vs-all microbial genomes

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).

🐣 locally query the ncbi taxonomy

MiGA: Microbial Genomes Atlas

Gtdb Taxdump ⭐ 29

GTDB taxonomy taxdump files with trackable TaxIds

Multitax ⭐ 23

Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)

Phantasm ⭐ 20

PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes

Whokaryote ⭐ 17

Classify metagenomic contigs as eukaryotic or prokaryotic

Pytaxonkit ⭐ 17

Python bindings for the TaxonKit library

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.

Pyfastani ⭐ 14

Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.

PyO3 bindings and Python interface to skani, a method for fast fast genomic identity calculation using sparse chaining.

Fast and space-efficient taxonomic classification of long reads

Dadaist2 ⭐ 11

Dadaist2 🟨 Highway to R

Taxonomy.jl ⭐ 10

Julia package to handle the NCBI Taxonomy database.

Background depletion/extraction using k-mer and/or alignment methods 🐼

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