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

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.

Install Conda using Miniforge3 script

SLURM Lightweight Automated Manager

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

Materials for Learning Bioinformatics and Enhancing Competencies - Conda

dojo snakemake assemblage long reads

Cruise Repository for Data Acquisition and Processing

Long-read sequencing is a highly accurate approach that can be used to challenging genomes, such as those containing stretches of highly repetitive elements and lot of structural variant. Long read sequencing can also be used to generate de novo assembly and genome finishing applications Lot of tools are used to make genome assembly with long reads every day and sometimes you don't know wich Assembler tool is the best for your organism. PodiumASM is here for you ! PodiumASM is is an open-source, scalable, modulable and traceable snakemake pipeline, able to compare multiple long read assemblies obtained from multiple assemblers tools. The workflow PodiumASM can help you to choose the best assemblies among all possibilities.