Taxonomic Classification Python Packages

sourmash

Quickly search, compare, and analyze genomic and metagenomic data sets.

microview

Generate reports from metagenomics data

crest4

The `crest4` python package can automatically assign taxonomic names to DNA sequences obtained from environmental sequencing.

paroxython

Search Python code for algorithmic features

kraken-biom

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).

vclust

Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes

gtnet

A package for running Genome Taxonomy Network predictions

filter-classified-reads

Filter for reads from taxa of interest using Kraken2/Centrifuge classification results.

xlassify

An alignment-free deep-learning model trained to classify human gut bacteria

icb

This library provides a way to parse, manipulate and analyze ICB and GICS Codes.

clark-biom

Create BIOM-format tables (http://biom-format.org) from CLARK output (http://clark.cs.ucr.edu/) for use with downstream tools such as UniFrac, iTol (itol.embl.de), or PhyloToAST (phylotoast.org), PhyloToAST (http://phylotoast.org).

flextaxd

FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )

taxamatcher

Correlates target taxonomy(i.e consensus lineages) with a reference taxonomy such as Greengenes, SILVA, etc.