nf-core pipeline ·
nf-core/phageannotator
Identifies, annotates, and quantifies bacteriophage sequences from genomic and metagenomic assemblies.
What nf-core/phageannotator is
nf-core/phageannotator is a bioinformatics pipeline designed to detect, annotate, and quantify bacteriophage sequences within genomic and metagenomic datasets. It was originally developed by CarsonJM within the nf-core framework to provide a standardised, reproducible workflow for viral analysis.
Metagenomic assemblies often contain complex mixtures of host and viral contigs that require specialised detection and filtering. The pipeline addresses this by coupling automated viral sequence detection and quality evaluation with host prediction, lifestyle classification, and abundance calculation.
What the pipeline does
The core identification and quantification module accepts metagenomic assemblies—such as those produced by nf-core/mag—and detects phage sequences de novo using geNomad, with optional reference-based matching using mash. Sequences undergo quality assessment and filtering via CheckV, followed by average nucleotide identity (ANI) dereplication with BLAST and CheckV, and binning via VRhyme. Phage abundances are quantified using bowtie2 and CoverM, with optional modules for strain-level profiling via inStrain and prophage activity estimation via propagAtE.
The annotation module classifies phage contigs through geNomad marker-based taxonomy and mash genome-proximity taxonomy. Host prediction is executed with iPHoP, temperate or virulent lifecycle prediction is carried out with BACPHLIP, and protein-coding genes are identified using Prodigal-gv.
Key facts
- Workflow manager
- Nextflow (>=22.10.1)
- Original author
- @CarsonJM
- Primary input
- (Meta)-genomic assemblies
- Viral identification
- geNomad, mash
- Quality control and dereplication
- CheckV, BLAST
- Binning
- VRhyme
- Abundance quantification
- bowtie2, CoverM
- Host and lifestyle prediction
- iPHoP, BACPHLIP
- Gene prediction
- Prodigal-gv
What you can use it for
- Metagenomic Phage Discovery
- Identifies viral contigs de novo from metagenomic assemblies using geNomad or against reference databases using mash.
- Phage Host and Lifestyle Prediction
- Infers prospective bacterial host species using iPHoP and determines whether phages are lytic or lysogenic using BACPHLIP.
- Viral Abundance Profiling
- Maps reads using bowtie2 and calculates coverage across samples with CoverM to generate inputs for differential abundance analysis.
- Prophage Activity Detection
- Evaluates active prophage sequences integrated into bacterial host genomes using propagAtE.
- Viral Protein Prediction
- Annotates protein-coding open reading frames across phage genomes using Prodigal-gv for downstream functional analysis.
Run it here
The research agent runs nf-core/phageannotator with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
Strengths and limits
Good at
- Integrates discovery, quality evaluation, taxonomy, lifestyle prediction, and abundance estimation in one continuous workflow.
- Combines both de novo sequence identification and reference-guided matching.
- Produces direct inputs for companion nf-core pipelines, including nf-core/differentialabundance and nf-core/funcscan.
- Provides optional modules for high-resolution strain profiling and prophage activity assessment.
Watch out for
- Requires pre-assembled (meta)-genomic sequences as primary input rather than working directly from unaligned reads for viral identification.
- Relies on external curated reference databases for tools such as geNomad, CheckV, and iPHoP.
Questions
Can I run nf-core/phageannotator without my own cluster?
The research agent runs nf-core/phageannotator with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/phageannotator under?
MIT, like every nf-core pipeline.
What inputs does the pipeline accept?
It takes genomic or metagenomic assemblies, such as those output by the nf-core/mag pipeline, along with read data for abundance calculations.
How are phage hosts predicted?
Host associations are determined computationally using iPHoP within the annotation workflow.
Can the pipeline assess whether a phage is temperate or lytic?
Yes, BACPHLIP is integrated into the annotation steps to predict phage lifestyle.
Which downstream pipelines can ingest output from nf-core/phageannotator?
Abundance tables from CoverM can feed into nf-core/differentialabundance, and protein-coding gene predictions from Prodigal-gv can feed into nf-core/funcscan.
How to cite it
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
Written from nf-core/phageannotator's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.