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GeVarLi pipeline for AFROSCREEN ANRS

dojo snakemake assemblage long reads

Reads Quality Control (RQC) allow raw NGS reads quality control, before continue with more downstream analysis.

This pipeline is an automatic structural annotation workflows written in snakemake. The annotation is based on two tools which uses RNA-Seq and/or protein homology information for predict coding sequence. One of this tools is BRAKER which use GeneMark-EX and AUGUSTUS. And the other tool is AUGUSTUS alone for improve annotation of small coding sequences with few or no intron. Before the annotation, the repeat element of genome are masked for avoid annotation probleme. In addition this workflows can perform a illumina assembly with ABySS using différent value of kmere.

snakemake workflow for mappind single/paired datas

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.

SLURM Lightweight Automated Manager

Materials for Learning Bioinformatics and Enhancing Competencies - Conda

Annotation of virulence factor of fungi (Effector , Cazyme ...)

Cruise Repository for Data Acquisition and Processing

Le Dockerfile de MariaDB 5.5 (20171210) mais sans le volume.