nf-core pipeline · archived · genome-assembly, metagenomics, variant-calling
nf-core/vipr
Viral genome assembly and intrahost low-frequency variant calling pipeline.
What nf-core/vipr is
nf-core/vipr is a bioinformatics analysis pipeline designed for de novo assembly and intrahost or low-frequency variant calling from viral sequencing samples. It was originally created by Andreas Wilm at the Genome Institute of Singapore as an ecosystem built around the LoFreq variant caller, progressing through several earlier iterations before being adapted for nf-core.
Analysing viral genetic material often requires separating true intrahost viral diversity from host contamination and sequencing artefacts. The pipeline handles this by standardising the processing pathway from quality trimming and decontamination to metagenomic classification, contig generation, and variant detection.
The pipeline has been archived and is no longer maintained.
What the pipeline does
The workflow begins by trimming and combining read pairs per sample and assessing quality using Skewer and FastQC. Host and non-target sequences are subsequently removed with decont, after which Kraken performs taxonomic classification to assess sample purity.
Following quality and contamination checks, BBtools Tadpole performs assembly to construct contigs, which are refined using ViPR Tools. Reads are mapped back to the assembly using BWA and LoFreq. Low-frequency variants are identified using LoFreq, and final coverage and variant allele frequency plots are produced using Bedtools and ViPR Tools.
Key facts
- Original developer
- Andreas Wilm (Genome Institute of Singapore)
- Workflow engine
- Nextflow
- Status
- Archived (no longer maintained)
- De novo assembler
- BBtools Tadpole
- Variant caller
- LoFreq
- Read aligner
- BWA
- Quality control and trimming
- FastQC, Skewer
- Taxonomic classification
- Kraken
What you can use it for
- Intrahost viral variant identification
- Detect low-frequency intrahost genetic variants in viral sequencing datasets using LoFreq.
- Viral genome assembly
- Assemble reads into contiguous sequences using BBtools Tadpole and polish the resulting contigs using ViPR Tools.
- Sample purity and taxonomic classification
- Screen viral sequencing samples for contaminants and assess composition with decont and Kraken.
Strengths and limits
Good at
- Specialises in resolving low-frequency and intrahost variants within viral populations using LoFreq.
- Encompasses an end-to-end workflow from read cleaning and contamination removal to assembly and variant visualization.
- Provides containerised software environments via Docker and Singularity for reproducible execution.
Watch out for
- The repository is archived and receives no further development or updates.
- Pre-assembly filtering relies specifically on the decont and Kraken tools rather than alternative taxonomic classifiers.
Questions
Can I run nf-core/vipr without my own cluster?
The research agent runs nf-core/vipr 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/vipr under?
MIT, like every nf-core pipeline.
What tools are used to call viral variants in this pipeline?
The pipeline uses LoFreq for both mapping reads to the assembly and detecting low-frequency variants.
How does the pipeline assemble viral genomes?
It uses Tadpole from BBtools to assemble reads into contigs, followed by polishing via ViPR Tools.
Is nf-core/vipr actively maintained?
No, the pipeline has been archived and is no longer maintained.
Written from nf-core/vipr's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.