VAPER is a viral (meta-)assembly pipeline that can:
🧬 Assemble genomes from complex samples, supporting multiple assemblies per sample (e.g., co-infections)
🧬 Automatically detect and select reference genomes
🧬 Predict the taxonomy of each assembly, with an optional viral metagenomic summary
🧬 Export reads associated with each assembly for downstream use
While VAPER was originally designed for hybrid capture data (e.g., Illumina VSP or Twist CVRP), it has also been used with shotgun metagenomic and tile-amplicon data. It comes stock with comprehensive reference sets for multiple taxa, including influenza A, SARS-CoV-2, and Monkeypox (full list). Keep on reading to learn more!
See the docs for more information.
VAPER would not be possible without the following people:
- Holly Halstead (WA PHL)
- Pauline Trinh (WA MEP)
- Allison Black (WA MEP)
- Stephanie Lunn (WA MEP)
- Kristen Waterman (WA PHL)
- Brandi Torrevillas (WSU)
VAPER was originally written by Jared Johnson for the Washington State Department of Health.