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

• UpdatedMar 12, 2025
• Python

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

• UpdatedMay 26, 2025
• C++

TAXnomic Profile Aggregation and STAndardisation

• UpdatedOct 31, 2024
• Python

Accurate, resource-frugal and deterministic DNA sequence classifier.

• UpdatedJul 9, 2025
• Python

Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets

• UpdatedMay 27, 2025
• Python

This repository contains all CWL descriptions of the MGnify pipeline version 5.0.

• UpdatedOct 24, 2024
• HTML

🐴 CLinically Okay Metagenomic Pipeline 🐴

• UpdatedOct 4, 2019
• Python

Genestrip - Efficient read classification, filtering and k-mer counting for selected groups of species

• UpdatedJul 12, 2025
• Java

XGBoost implementation for bacteria family identification

• UpdatedJun 26, 2025
• Python

• UpdatedDec 14, 2018

subset and spaced seed design tool

• UpdatedMay 23, 2025
• C++

Accurate taxonomic classification and abundance profiling using locality-sensitive hashing.

• UpdatedApr 1, 2024
• C++

discover-virome: identify and quantify viruses from metagenomic assemblies

• UpdatedJan 20, 2022
• Python

Code associated with Werbin et al. 2022, F1000 Research

• UpdatedMar 8, 2021
• R

A selection of databases for Genestrip

• UpdatedJun 4, 2025
• Shell

The Genome Taxonomy Network for assigning microbial taxonomy to DNA sequences

• UpdatedMar 5, 2024
• Python

The impact of transitive annotation on the training of taxonomic classifiers

• UpdatedMar 23, 2024
• Jupyter Notebook

Contains all the code and data related to the CS6024 - Algorithmic Approaches to Computational Biology in the topic: Disease detection using metagenomic dataset

• UpdatedMay 15, 2024
• Jupyter Notebook