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VAPER: Viral Assembly from Probe-based EnRichment

Overview

VAPER is a pipeline for virus genome assembly.

Key Features:

• 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)
• Predicts the taxonomy of each assembly (Also includes a metagenomic summary!)
• Reads associated with each assembly are exported for downstream use
• Can utilize iVar or IRMA assemblers (IRMA modules built on the fly!)

Automated Reference Selection:

VAPER comes with comprehensive reference sets for the following viral taxa (created using EPITOME):

Taxon	Segments	No. References	No. Species	No. Input Sequences
Alphacoronavirus	wg	201	67	1040
Alphainfluenzavirus	1 - 8	2394	1	484876
Betacoronavirus	wg	140	53	3566
Betainfluenzavirus	1 - 8	94	1	96657
Bocaparvovirus	wg	104	48	608
Enterovirus	wg	1967	26	6740
Hantavirus	l, m, s	244	32	825
Hepacivirus	wg	888	42	1060
Hepatovirus	wg	60	14	114
Lyssavirus	wg	198	23	2126
Mastadenovirus	wg	128	73	1507
Metapneumovirus	wg	28	4	420
Morbillivirus	wg	100	14	1176
Norovirus	wg	284	5	1148
Orthoflavivirus	wg	428	83	7960
Orthopneumovirus	wg	22	4	18344
Orthopoxvirus	wg	15	13	7885
Orthorubulavirus	wg	38	9	1053
Respirovirus	wg	51	17	531

Click here to learn more about these references.