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GeVarLi : GEnome assembly, VARiant calling and LIneage assignation. https://transvihmi.pages.ird.fr/nfernandez/GeVarLi/en

A, still very experimental, R package that acts as a storage location for functions and interfaces in connection with genomics (genomes, transcriptomes, annotation, phylogenomics, ...)

snakemake workflow for mappind single/paired datas

GraTools is a powerful tool for analyzing and handling pangenome graphs quickly, whatever the model' and therefore the size and the complexity of the GFA file. It allows users to extract sequences or subgraphs, convert graphs into FASTA sequences, and identify shared and specific nodes across samples. Additionally, it provides essential statistics for chromosomes and samples data. With multi-threading support and flexible logging capabilities, Gratools is an efficient solution for pangenome graph analysis.

Cruise Repository for Data Acquisition and Processing

dojo snakemake assemblage long reads

Install Conda using Miniforge3 script

SLURM Lightweight Automated Manager

Materials for Learning Bioinformatics and Enhancing Competencies - Conda