VAPER: Viral Assembly from Probe-based EnRichment

Key Features

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, it has also been used with shotgun metagenomic and tile-amplicon data. It comes stock with a comprehensive reference set for thousands of viral species, including all species targeted by the Illumina VSP v2.0 panel (see the full list here).

Pipeline Overview

More Information:

See the docs for more information.

Acknowledgements

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.