This workflow performs core genome multilocus sequence typing (cgMLST) on contigs corresponding to one bacterial genome to characterize bacterial strains using curated reference schemes.

Metagenomic analysis, from raw reads to gene catalog. Uses Megahit to assemble contigs and Prodgial to predict CDSs on contigs to provide the gene catalog. Finally, functional, taxonomic, and antimicrobial resistance information is provided.

MAGNETO is an automated snakemake workflow dedicated to MAG (Metagenome-Assembled Genomes) reconstruction from metagenomic data.

It includes a fully-automated coassembly step informed by optimal clustering of metagenomic distances, and implements complementary genome binning strategies, for improving MAG recovery.

Key Features

• Quality Control (QC): Automatically assesses the quality and the contamination of input reads, ensuring that low-quality data are filtered out to improve downstream ...

This project is an analysis pipeline using Snakemake for RNAseq analysis in order to find differentially expressed genes. It has been widely tested on human RNA sequencing from an Illumina HiSeq but should work on most systems and many other species, provided the necessary resource files can be downloaded.

Description

This pipeline is set for paired-end data only from Illumina HiSeq output files.

The main steps of the pipeline are:

• optionnal cleaning data with ...