Taxonomic Classification Python Packages

sourmash

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

deeptaxa-rrna

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

microview

Generate reports from metagenomics data

crest4

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

paroxython

Tag and recommend Python exercises based on 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).

gtnet

The Genome Taxonomy Network for assigning microbial taxonomy to DNA sequences

filter-classified-reads

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

vclust

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

icb

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

xlassify

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

clark-biom

Create BIOM-format tables from CLARK abundance tables.

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

Easy to use taxonomy correlator