nf-core/phageannotator

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Introduction

nf-core/phageannotator is a bioinformatics pipeline for identifying, annotation, and quantifying phage sequences in (meta)-genomic sequences.

Pipeline summary

The core identification/quantification portion of this pipeline takes (meta)-genomic assemblies (as output by nf-core/mag) and performs the following steps:

1. Phage sequence identification
   • de novo identification (geNomad)
   • OPTIONAL - reference-based identification (mash)
2. Quality assessment/filtering (CheckV)
3. ANI clustering/dereplication (BLAST)(CheckV)
4. Binning (VRhyme)
5. Abundance estimation (bowtie2)(CoverM)
   • Output can be used as input for nf-core/differentialabundance
6. OPTIONAL - Strain profiling (inStrain)
7. OPTIONAL - Prophage activity prediction (propagAtE)

The annotation portion of this pipeline performs the following steps:

1. Marker-based taxonomic classification (geNomad)
2. Genome proximity taxonomic classification (mash)
3. Host prediction (iPHoP)
4. Lifestyle prediction (BACPHLIP)
5. Protein-coding gene prediction (Prodigal-gv)
   • Output can be used as input for nf-core/funcscan

Quick Start

1. Install Nextflow (>=22.10.1).

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 nf-core/phageannotater -profile test,YOURPROFILE --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.

4. Start running your own analysis!

   nextflow run nf-core/phageannotater --input samplesheet.csv --outdir <OUTDIR> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>

   nf-core/phageannotator is a bioinformatics pipeline that …

1. Read QC (FastQC)
2. Present QC for raw reads (MultiQC)

Usage

Now, you can run the pipeline using:

nextflow run nf-core/phageannotator \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

see docs.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Documentation

The nf-core/phageannotater pipeline comes with documentation about the pipeline usage, parameters and output.

Credits

nf-core/phageannotator was originally written by @CarsonJM.

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.

For further information or help, don’t hesitate to get in touch on the Slack #phageannotator channel (you can join with this invite).

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.