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VAPER: Viral Assembly from Probe-based EnRichment

VAPER is a viral assembly pipeline. Key features include:

  • Builds assemblies from probe enrichment (a.k.a hybrid capture/enrichment), shotgun metagenomic, and tiled-amplicon sequence data
  • Automated reference selection (Detects what is in your sample)
  • Can generate multiple assemblies per sample (Useful for co-infections)
  • Can utilize iVar or IRMA assemblers (IRMA modules built on the fly!)
  • Reads associated with each assembly are exported for downstream use
  • Provides a metagenomic summary of dominant viral taxa

VAPER comes with comprehensive reference sets for the following viral species (created using EPITOME):

Taxon Segments Input Sequences No. References Data Source
Influenza A 1-8 78703 (per segment) 8-93 GISAID
Influenza B 1-8 17401 (per segment) 1-2 GISAID
Measles morbillivirus wg 890 1 NCBI
Mumps orthorubulavirus wg 1343 1 NCBI
Lyssavirus rabies wg 2607 42 NCBI
Norovirus wg 1662 87 NCBI
Respiratory Syncytial Virus wg 15273 2 GISAID
West Nile virus wg 1993 8 NCBI
Enterovirus D68 wg 590 4 NCBI
Hepacivirus wg 1245 120 NCBI
Hepatovirus wg 131 20 NCBI
Monkeypox virus wg 2129 1 NCBI
Severe acute respiratory syndrome coronavirus wg 2000 (random) 1 NCBI

See the wiki for more information.

VAPER was originally written by Jared Johnson for the Washington State Department of Health.

Quick Start

Step 1: Prepare your samplesheet

Note: Nextflow requires absolute file paths. samplesheet.csv:

sample,fastq_1,fastq_2
sample01,sample01_R1_001.fastq.gz,sample01_R2_001.fastq.gz
sample02,sample02_R1_001.fastq.gz,sample02_R2_001.fastq.gz

Step 2: Run VAPER

Note: This will use the default reference set. You can provide your own reference set using the --refs parameter.

nextflow run DOH-JDJ0303/VAPER \
    -r main \
    -profile <docker/singularity/.../institute> \
    --input samplesheet.csv \
    --outdir results \
    --max_cpus 8 \
    --max_memory 16.GB

Acknowledgements

VAPER would not be possible without the following people:
Holly Halstead (WA PHL) (check out her tool varcraft!)
Pauline Trinh (WA MEP)
Allison Black (WA MEP)
Stephanie Lunn (WA MEP)
Kristen Waterman (WA PHL)