Introduction

nf-core/nfvibrio is a bioinformatics best-practice analysis pipeline for Vibrio parahaemolyticus analysis. This workflow is under active development and updates. If you are using it (thank you!) remember to keep your fork updated by regularly syncing it.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.

Pipeline summary

1. Read QC (FastQC)
2. Performing read QC (FASTP)
3. Assemble quality controlled reads (SHOVILL)
   1. Estimating genome size by counting unqiue kmer-mers (KMC)
   2. Correct sequencing errors in reads (Lighter)
   3. Merge paired-end reads (FLASH)
   4. Assemble with (SPAdes)/(SKESA)/(Megahit) with modified kmer range
   5. Correct minor assembly errors by mapping reads back to contigs (PILON)
4. Perform assembly QC (QUAST)
5. Annotate assembled contigs (PROKKA)
6. Find antimicrobial resistance genes and point mutations in assembled contigs (AMRFINDERPLUS)
7. Scan contig files against traditional PubMLST typing schemes (MLST)
8. Present QC for raw reads (MULTIQC)

Quick Start

1. Install Nextflow (>=21.0.0)

2. Install any of Docker, Singularity (you can follow this tutorial), Podman, Shifter or Charliecloud for full pipeline reproducibility (you can use Conda both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see docs).

3. Download the pipeline and test it on a minimal dataset with a single command:

   nextflow run nfvibrio/main.nf -profile <conda,singularity,YOURPROFILE>  --genome "VP01" --input sample_sheet.csv --outdir <OUTDIR> --assembler <skesa,megahit,spades>

   Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (YOURPROFILE in the example command above). You can chain multiple config profiles in a comma-separated string.

   • The pipeline comes with config profiles called docker, singularity, podman, shifter, charliecloud and conda which instruct the pipeline to use the named tool for software management. For example, -profile test,docker.
   • Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.
   • If you are using singularity, please use the nf-core download command to download images first, before running the pipeline. Setting the NXF_SINGULARITY_CACHEDIR or singularity.cacheDir Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
   • If you are using conda, it is highly recommended to use the NXF_CONDA_CACHEDIR or conda.cacheDir settings to store the environments in a central location for future pipeline runs.

Documentation

Currently this README serves as the only documentation for this workflow. More detailed documentation is under development. If you have specific questions, open a issue or connect at [email protected].

Credits

nf-core/nfvibrio was originally written by Muhammad Zohaib Anwar under the supervision of William Hsiao at the Centre for Infectious Disease Genomics and One Health at Simon Fraser University.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.