Metagenomic classifers

HOPS

A pipeline which focuses on screening MALT data for the presence of a user-specified list of target species.

MALT

A sequence alignment and analysis tool designedfor processing high-throughput sequencing data, especially in the context of metagenomics.

metabit

An integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data.

SPARSE

Indexes >100,000 reference genomes in public databases in to hierarchical clusters and uses it to predict origins of metagenomic reads.