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Jared Johnson edited this page Jul 16, 2024
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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 | Data Source |
|---|---|---|---|
| Influenza A | 1-8 | 78703 (per segment) | GISAID |
| Influenza B | 1-8 | 17401 (per segment) | GISAID |
| Measles morbillivirus | wg | 890 | NCBI |
| Mumps orthorubulavirus | wg | 1343 | NCBI |
| Lyssavirus rabies | wg | 2607 | NCBI |
| Norovirus | wg | 1662 | NCBI |
| Respiratory Syncytial Virus | wg | 15273 | GISAID |
| West Nile virus | wg | 1993 | NCBI |
| Enterovirus D68 | wg | 590 | NCBI |
| Hepacivirus | wg | 1245 | NCBI |
| Hepatovirus | wg | 131 | NCBI |
| Monkeypox virus | wg | 2129 | NCBI |
| Severe acute respiratory syndrome coronavirus | wg | 2000 (random) | NCBI |