MPOA | Workflow to mask pathogens for outbreak analysis

Citation:

Nanopore sequencing for accurate bacterial outbreak tracing
Mara Lohde, Gabriel E. Wagner, Johanna Dabernig-Heinz, Adrian Viehweger, Sascha D. Braun, Stefan Monecke,Celia Diezel, Claudia Stein, Mike Marquet, Ralf Ehricht, Mathias W. Pletz, Christian Brandt
https://www.biorxiv.org/content/10.1101/2023.09.15.556300v2

What is this Repo?

• A quick workflow to mask fasta files for outbreak analysis
• It mitigates false base calls from e.g., modified bases by masking all such positions that are "uncertain"
• Figures and overviews are provided to assess weather your samples might be affected by such an issue

Documentation

https://maralohde.github.io/MPOA-documentation/

Quick installation

1.1 Nextflow (the workflow manager)

• MPOA needs Nextflow and java run time (default-jre)
  • install java run time via: sudo apt install -y default-jre
  • install Nextflow e.g.: curl -s https://get.nextflow.io | bash && sudo mv nextflow /bin && sudo chmod 770 /bin/nextflow

1.2 Docker

• Installation here (recommended), alternatively via: sudo apt install -y docker
• Add Docker to the user: sudo usermod -a -G docker $USER

1.3 Singularity

• As an alternative to Docker you can also install and use Singularity, e.g. on a HPC
• Installation here
• Note, that with Singularity the following environment variables are automatically passed to the container to ensure execution on HPCs: HTTPS_PROXY, HTTP_PROXY, http_proxy, https_proxy, FTP_PROXY and ftp_proxy.

Quick start

• Reads and genomes are matched by their name before the first "."
• E.g. genome file sample1.test.fasta matches with read file sample1.fastq.gz

#install
nextflow pull replikation/MPOA

#help
nextflow run replikation/MPOA -profile local,docker --help

#example run
nextflow run replikation/MPOA --fastq '*.fastq' --fasta '*.fasta' -profile local,docker

#example run on a HPC
nextflow run replikation/MPOA --fastq '*.fastq' --fasta '*.fasta' -profile slurm,singularity