The Clin-mNGS pipeline is an integrated, open-source, scalable, reproducible, and user-friendly framework scripted using the Snakemake workflow management software. The implementation avoids the hassle of manual installation and configuration of the multiple command-line tools and dependencies and can be deployed on most Linux workstations and clusters. The versions of the implemented tools are made user modifiable. The approach directly screens pathogens from clinical raw reads and generates consolidated reports for each sample.

The pipeline is currently automated to perform in quality check, filtering, host subtraction, assembly of reads into contigs, assembly metrics, relative abundances of bacterial species, antimicrobial resistance genes, plasmid finding, and virulence factors identification.

Commands to start analysing your data:

conda create -c conda-forge -c bioconda -n snakemake snakemake      
conda activate snakemake
snakemake --use-conda --cores 16