UCT-srst2: MLST (and antimicrobial resistance/ virulence factor) analysis using srst2, implemented in Nextflow
This pipeline accepts raw (or trimmed) reads in .fastq format and performs MLST (and optional AMR or virulence factor) analyses using srst2 (https://github.com/andrewjpage/docker_mlst/tree/master/srst2). Implemented for the Ilifu (slurm) cluster, which can be modified by adding a custom config file. The srst2 singularity image used was obtained here https://quay.io/repository/biocontainers/srst2?tab=tags
The typical command for running the pipeline is as follows:
nextflow run kviljoen/uct-srst2 --reads '*_R{1,2}.fastq.gz' -profile ilifu --mlst_db Pseudomonas_aeruginosa.fasta --mlst_definitions paeruginosa.txt --mlst_delimiter '_' --AMR_db ARGannot_r3.fasta --outdir Ps_aerug_srst2_MLST
Mandatory arguments:
--reads Path to input data (must be surrounded with quotes!)
-profile Hardware config to use. ilifu OR standard
--outdir Specify folder where results should be written to (will be created if non-existent)
srst2 options:
--mlst_delimiter Default="-" you may have to change to e.g. "_" depending on the format of your mlst reference file
--mlst_db Fasta file of MLST alleles (can be downloaded with getmlst.py from srst2 e.g. getmlst.py --species "Escherichia coli"
--gene_db Antimicrobial resistence (or other e.g virulence) gene DB (Fasta) (can be downloaded from https://github.com/katholt/srst2/tree/master/data or created)
Help:
--help Will print out summary above when executing nextflow run kviljoen/uct-srst2 --help
Nextflow (0.27.6 or higher), all other software/tools required are contained in the (platform-independent) singularity image for srst2, which can be obtained here https://quay.io/repository/biocontainers/srst2?tab=tags
For detailed information please see https://github.com/katholt/srst2
This project is licensed under the MIT License - see the LICENSE.md file for details