Introduction

maxibor/corephylo is a bioinformatics best-practice analysis pipeline for core-genome based phylogenetic analysis.

mermaid graph LR; A[fasta genomes] -->|Bakta <br> functional annotation | B[GFF3 functional annotations] B -->|PANAROO <br> pangenome computation| C[Fasta core genomes alignment] C -->|ClonalFrameML + maskrc-svg.py <br> mask recombinant regions| D[Non recombinant core genomes alignment] D -->|IQTree <br> ML phylogenetic analysis| E[ML Phylogenetic tree] D -->|RapidNJ <br> NJ phylogenetic analysis| F[NJ Phylogenetic tree] D -->|SNP-sites <br> SNPs extraction| G[VCF] D -->|snp-dists <br> pairwise distance computation| H[SNPs based pairwise distance matrix]

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. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

Quick Start

1. Install Nextflow (>=21.10.3)

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:

bash nextflow run maxibor/corephylo -profile test,YOURPROFILE --bakta-db <path-to-bakta-db> --outdir <OUTDIR>

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.

1. Start running your own analysis!

<!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->

bash nextflow run maxibor/corephylo --genome genomesheet.csv --bakta-db <path-to-bakta-db> --outdir <OUTDIR> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>

Documentation

• Usage
• Parameters

Credits

maxibor/corephylo was originally written by Maxime Borry.

We thank the following people for their extensive assistance in the development of this pipeline:

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.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

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.