GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Bugcrowd’s baseline priority ratings for common security vulnerabilities

Taxonomies used in MISP taxonomy system and can be used by other information sharing tool.

Application and Python module for average nucleotide identity analyses of microbes.

This is the repository for the BioCLIP model and the TreeOfLife-10M dataset [CVPR'24 Oral, Best Student Paper].

🐞 Convert NCBI taxonomy dump into lineages

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

Local version of the virus identification and analysis web server (tool set)

Open-source description language for privacy to declare data types and data behaviors in your tech stack in order to simplify data privacy globally. Supports GDPR, CCPA, LGPD and ISO 19944.

A tool for drawing ANI clustermap between all-vs-all microbial genomes

The source code used for self-supervised taxonomy expansion method TaxoExpan, published in WWW 2020

Code for paper "End-to-End Reinforcement Learning for Automatic Taxonomy Induction", ACL 2018

Topic Inference with Zeroshot models

TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various use-cases of mNGS in mind.

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

Identify plants, birds, and insects in photos. Should an identification to species be unsuccessful, an identification to a higher taxonomic level - like genus, family, or order - is made.

Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)

Python bindings for the TaxonKit library

Full resources supporting the publication "A Pragmatic Guide to Geoparsing Evaluation."

Tag your nature photos with iNat taxonomy and observation metadata