kmer based feature extraction tool for bioinformatics, metagenomics, AI/ML and more

Snakemake-based pipeline for metagenomics classification. Currently support short-reads Illumina Sequences and long-reads ONT Sequences.

Graph-based assembly phasing

TrIdent- Transduction Identification: Automatic detection, classification and characterization of active transduction events in microbiomes.

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

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

Metagenotyping analysis in R

Some useful python scripts for biologists

MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.

Repository for the presentation of work developed by the student Duarte Velho for the UC Project, of the Master in Bioinformatics of the University of Minho, academic year 23-24.

This repository contains all project files, including scripts, results, and articles. It was developed for the UC project included in the bioinformatics master's program for 2023-2024.

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

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.

Reconstruction and analysis of viral and host genomes at multi-organ level

Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly

A collection of Galaxy-related training material

Assembly and binning of metagenomes

🦠📇 Compare prokaryotic genomic assemblies

Deepurify is a tool to filter the contaminated contigs in a MAG with a language model.

An analysis and visualization platform for 'omics data