VAPER (Viral Assembly from Probe-based Enrichment) 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
🧬 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 62 viral taxa, including all species targeted by the (see the full list ). Check out the documentation page to learn more!
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