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VAPER: Viral Assembly from Probe-based EnRichment

VAPER creates consensus-based assemblies from probe enrichment (a.k.a hybrid capture/enrichment) and shotgun metagenomic sequence data. One strength is it can handle samples containing multiple viral species and/or subtypes. When multiple viruses are present, VAPER will generate a consensus assembly for each, so long as an appropriate reference genome is supplied and the estimated genome fraction exceeds the minimum threshold (default: 50%). To ensure all relevant species are captured, VAPER supplies a summary of all viral sequences in the sample using Sourmash.

VAPER requires the following inputs:

1. Paired-end Illumina reads.
2. One or more reference assemblies for your species of interest.

VAPER was designed to use references created by the EPITOME pipeline, which attempts to condense the diversity of viral species into a set of discrete reference assemblies. That said, there is nothing keeping you from supplying VAPER with your own reference assemblies and/or adding references to the set created by EPTIOME.