mourisl/centrifuger

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

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

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

ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.

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

SemiBin: metagenomics binning with self-supervised deep learning

The second version of the Kraken taxonomic sequence classification system

Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes

Versatile open-source tool for microbiome analysis