shenwei356/taxonkit

A Python package for obtaining complete lineages and the lowest common ancestor (LCA) from a set of taxonomic identifiers

Bonsai: Fast, flexible taxonomic analysis and classification

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

genome_updater is a bash script that downloads and updates (non-redundant) snapshots of the NCBI Genomes repository (RefSeq/GenBank) with advanced filters, detailed logs and reports, file integrity checks, NCBI taxonomy and GTDB integration and support for parallel downloads.

REference Sequence annotation and CuRatIon Pipeline

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

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

Microbiome classification pipeline

Kun-peng: an ultra-fast, low-memory footprint and accurate taxonomy classifier for all