Bioinformatics tools and workflows

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.

Another Gff Analysis Toolkit. Suite of tools to handle gene annotations in any GTF/GFF format.

Software to convert GFF3 and fasta to legal EMBL format suitable for the submission to the European Nucleotide Archive (ENA) database.

Software to guess the RNA-Seq library type of paired and single end read files using mapping and gene annotation.

IgDiscover analyzes antibody repertoires and discovers new V genes from high-throughput sequencing reads. Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes).

nf-core/Sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome.

TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample.

DEPICTER is an open-source interactive and web-based tool for annotating histopathology whole-slide images (WSI).

aMeta is a Snakemake workflow for identifying microbial sequences in ancient DNA shotgun metagenomics samples.

GenErode is a Snakemake pipeline that analyzes whole-genome sequencing data from historical and modern samples, with the aim to look for patterns of genome erosion.

nfcore/AmpliSeq is a bioinformatics pipeline for amplicon sequencing. It denoises amplicons and supports various taxonomic databases like 16S, ITS, CO1, and 18S.

nf-core/MetaboIGNITER is a workflow for pre-processing mass spectrometry-based metabolomics data.

Cutadapt is a tool that finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly.

nbis-meta is a snakemake workflow for paired- and/or single-end whole-genome shotgun metagenomic data.

A version of AlphaFold to better utilize partial experimental structures to build high-quality protein assemblies, including very large protein complexes

Strobealign is a read mapper that is typically significantly faster than other read mappers while achieving comparable or better accuracy