VAPER is a viral (meta-)genome assembly pipeline which we use for viral genome assembly at the Washington State Public Health Laboratory. 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 (in the event of a sample co-infection)
- Predicts the taxonomy of each assembly (Also includes a viral metagenomic summary!)
- Reads associated with each assembly are exported for downstream use
- Can utilize iVar or IRMA assemblers (IRMA modules built on the fly!)