nf-core/phageannotator
Introduction
*nf-core/phageannotator* is a bioinformatics pipeline for identifying, annotation, and quantifying phage sequences in (meta)-genomic sequences.
<p align="center"> <img src="https://raw.githubusercontent.com/nf-core/phageannotator/dev//docs/images/nf-core-phageannotator_workflow.png" alt="nf-core/phageannotator workflow overview" width="90%"> </p>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:
- Phage sequence identification
- Quality assessment/filtering (
CheckV
) - ANI clustering/dereplication (
BLAST
)(CheckV
) - Binning (
VRhyme
) - Abundance estimation (
bowtie2
)(CoverM
)- Output can be used as input for *nf-core/differentialabundance*
- OPTIONAL - Strain profiling (
inStrain
) - OPTIONAL - Prophage activity prediction (
propagAtE
)
The annotation portion of this pipeline performs the following steps:
- Marker-based taxonomic classification (
geNomad
) - Genome proximity taxonomic classification (
mash
) - Host prediction (
iPHoP
) - Lifestyle prediction (
BACPHLIP
) - Protein-coding gene prediction (
Prodigal-gv
)- Output can be used as input for *nf-core/funcscan*
Quick Start
-
Install
Nextflow
(>=22.10.1
). -
Install any of
Docker
,Singularity
(you can follow this tutorial),Podman
,Shifter
orCharliecloud
for full pipeline reproducibility (you can useConda
both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see docs). -
Download the pipeline and test it on a minimal dataset with a single command:
nextflow run nf-core/taxprofiler -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
andconda
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 eitherdocker
orsingularity
and set the appropriate execution settings for your local compute environment. - If you are using
singularity
, please use thenf-core download
command to download images first, before running the pipeline. Setting theNXF_SINGULARITY_CACHEDIR
orsingularity.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 theNXF_CONDA_CACHEDIR
orconda.cacheDir
settings to store the environments in a central location for future pipeline runs.
- The pipeline comes with config profiles called
-
Start running your own analysis!
nextflow run nf-core/taxprofiler --input samplesheet.csv --databases database.csv --outdir <OUTDIR> --run_<TOOL1> --run_<TOOL1> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
For more details and further functionality, please refer to the usage documentation and the parameter documentation.
Documentation
The nf-core/taxprofiler 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:
<!-- TODO nf-core: If applicable, make list of people who have also contributed -->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
<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. --> <!-- If you use nf-core/phageannotator for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) --> <!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->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.