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

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)