An all-in-one solution for streamlined metagenomic analyses.
MetaGEN is an all-in-one pipeline for the analysis of WGS shotgun metagenome data. MetaGEN takes raw paired-end NGS reads (.fastq.gz) as an input and will perform several analysis steps on these in order to produce a wide variety of outputs, including:
- QC reports
- Taxonomic tables
- Metagenomic assemblies (individual, co and bins)
- Resistome, virulence and plasmidome profiles
- Functional pathways and k-mers associated with each sample
MetaGEN requires Snakemake to run, which will install all other dependencies automatically.
- Clone the MetaGEN repository
- Copy read files into the "input" folder
- Make sure the paired-end reads are named "<unique_name>_R1.fastq.gz" and "<unique_name>_R2.fastq.gz" respectively
- Edit the config.yml as needed
- Run MetaGEN
This project is licensed under the GPLv3 Licence. See the LICENSE file for more details.