nf-core pipeline · chimeric-alignment, ctat, viral-integration
nf-core/viralintegration
Identifies viral integration sites in host genomes from sequencing reads using a chimeric read alignment strategy.
What nf-core/viralintegration is
nf-core/viralintegration is a bioinformatics analysis pipeline designed to identify viral integration events in host genomes using chimeric sequencing reads. The workflow is initially based on CTAT-VirusIntegrationFinder and automates the detection and verification of genomic junctions where viral sequences integrate into host chromosomes.
The pipeline was originally developed by Alyssa Briggs and Edmund Miller at The Functional Genomics Laboratory at The University of Texas at Dallas, with assistance from Tae Hoon Kim and Robert Allaway. It addresses the technical challenge of accurately distinguishing authentic viral insertion breakpoints from sequencing noise and artefacts.
By combining host read filtering, adapter and poly(A) trimming, chimeric alignment, and evidence verification, the pipeline provides researchers with annotated candidate integration sites, abundance metrics, and interactive visualisations.
What the pipeline does
The pipeline takes single-end or paired-end FASTQ reads defined in a samplesheet and conducts initial quality checks with FastQC before aligning reads to the host genome using STAR. Unaligned reads are extracted and processed through Trimmomatic for quality and adapter trimming, followed by PolyAStripper to remove poly(A) tails. These trimmed reads are then aligned to a combined host and viral reference index generated by STAR, and the resulting alignments are sorted and indexed using SAMtools to identify potential insertion site candidates.
Candidate chimeric reads undergo a verification process where chimeric genomic targets and annotations are extracted to build validation indices. Reads are re-aligned with STAR, sorted, indexed, and filtered to remove duplicate alignments. Chimeric contig evidence is quantified to generate refined abundance plots, tab-delimited insertion site summaries with reference gene annotations, and interactive browser-based genome viewers.
Key facts
- Pipeline engine
- Nextflow DSL2
- Algorithmic foundation
- CTAT-VirusIntegrationFinder
- Input formats
- Single-end or paired-end FASTQ (via samplesheet.csv)
- Primary aligner
- STAR
- Read processing tools
- Trimmomatic, PolyAStripper, SAMtools
- Quality control reporting
- FastQC, MultiQC
- Interactive viewers
- HTML files based on igv.js (VirusDetect.igvjs.html, vif.html)
- Primary outputs
- Annotated TSV insertion tables, abundance plots (PNG), BAM/BAI alignments
What you can use it for
- Viral insertion site identification
- Locate specific genomic coordinates where viral sequences have integrated into a host genome using sequencing reads.
- Gene annotation of integration breakpoints
- Evaluate which host genes and genomic features are interrupted by viral insertions using the pipeline's annotated TSV reports.
- Interactive visual inspection of candidate junctions
- Inspect alignment support and chimeric evidence across host and viral junctions using embedded igv.js HTML viewers.
- Viral read abundance profiling
- Quantify viral read counts and generate genome-wide abundance plots to evaluate viral presence in sequencing samples.
Run it here
The research agent runs nf-core/viralintegration 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
- Performs a two-tier chimeric verification step that re-aligns reads to extracted chimeric targets and removes PCR duplicates.
- Automates read cleaning on unaligned reads by combining quality trimming, adapter removal, and poly(A) stripping.
- Generates interactive HTML genome viewers alongside standard tabular output for direct visual validation of integration sites.
- Aggregates sequencing, trimming, and alignment statistics across samples into a single MultiQC report.
Watch out for
- Relies on chimeric reads spanning the host-viral boundary, requiring sufficient sequencing coverage across the integration junction.
- Requires reference FASTA sequences for both the host and candidate viral genomes.
Questions
Can I run nf-core/viralintegration without my own cluster?
The research agent runs nf-core/viralintegration 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/viralintegration under?
MIT, like every nf-core pipeline.
What input data does nf-core/viralintegration require?
It requires a CSV samplesheet specifying sample names and file paths to single-end or paired-end FASTQ sequencing files, along with host and viral reference genomes.
How does the pipeline detect chimeric host-viral reads?
It filters out reads mapping cleanly to the host genome, trims the unmapped reads, and aligns them against a merged host and viral reference index using STAR.
What interactive visualization tools are generated?
The pipeline outputs web-based interactive genome viewers based on igv.js, including VirusDetect.igvjs.html for viral infection evidence and vif.html for validated insertion sites.
How are duplicate alignments handled?
Duplicate alignments are removed during the chimeric read verification phase before chimeric contig evidence counts are calculated.
How to cite it
doi: 10.5281/zenodo.7783480
Written from nf-core/viralintegration's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.