Taxonomic Classification Python Packages

sourmash

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

microview

A reporting tool for aggregating results from taxonomic classification analyses

paroxython

Tag and recommend Python exercises based on algorithmic features

crest4

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

vclust

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

deeptaxa-rrna

Hybrid CNN-BERT deep learning for hierarchical taxonomic classification of 16S rRNA sequences

gtnet

The Genome Taxonomy Network for assigning microbial taxonomy to DNA sequences

kraken-biom

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

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.

filter-classified-reads

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

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).

taxamatcher

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

flextaxd

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