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

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

TAXnomic Profile Aggregation and STAndardisation

Accurate, resource-frugal and deterministic DNA sequence classifier.

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

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

kMetaShot is an alignment-free taxonomic classifier based on k-mer/minimizer counting for MAGs

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

🐴 CLinically Okay Metagenomic Pipeline 🐴

XGBoost implementation for bacteria family identification

subset and spaced seed design tool

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

discover-virome: identify and quantify viruses from metagenomic assemblies

Code associated with Werbin et al. 2022, F1000 Research

A selection of databases for Genestrip

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

The impact of transitive annotation on the training of taxonomic classifiers

The Genome Taxonomy Network for assigning microbial taxonomy to DNA sequences

Graph-Meta is a topology-aware learning framework designed to classify metagenomic contigs into four major biological classes: Prokaryotes, Viruses, Plasmids, and Microeukaryotes. By leveraging the assembly graph topology, the model resolves ambiguities in fragmented assemblies that traditional sequence-based classifiers often miss.