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VAPER: Viral Assembly from Probe-based EnRichment

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 an 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