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].
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
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
Local version of the virus identification and analysis web server (tool set)
Code for paper "End-to-End Reinforcement Learning for Automatic Taxonomy Induction", ACL 2018
Topic Inference with Zeroshot models
Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
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.
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
Tag your nature photos with iNat taxonomy and observation metadata
Full resources supporting the publication "A Pragmatic Guide to Geoparsing Evaluation."
Add a description, image, and links to the taxonomy topic page so that developers can more easily learn about it.
To associate your repository with the taxonomy topic, visit your repo's landing page and select "manage topics."