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 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	No. References	Data Source
Influenza A	1-8	78703 (per segment)	8-93	GISAID
Influenza B	1-8	17401 (per segment)	1-2	GISAID
Measles morbillivirus	wg	890	1	NCBI
Mumps orthorubulavirus	wg	1343	1	NCBI
Lyssavirus rabies	wg	2607	42	NCBI
Norovirus	wg	1662	87	NCBI
Respiratory Syncytial Virus	wg	15273	2	GISAID
West Nile virus	wg	1993	8	NCBI
Enterovirus D68	wg	590	4	NCBI
Hepacivirus	wg	1245	120	NCBI
Hepatovirus	wg	131	20	NCBI
Monkeypox virus	wg	2129	1	NCBI
Severe acute respiratory syndrome coronavirus	wg	2000 (random)	1	NCBI

See the wiki for more information.

VAPER was originally written by Jared Johnson for the Washington State Department of Health.

Quick Start

Step 1: Prepare your samplesheet

Note: Nextflow requires absolute file paths. samplesheet.csv:

sample,fastq_1,fastq_2
sample01,sample01_R1_001.fastq.gz,sample01_R2_001.fastq.gz
sample02,sample02_R1_001.fastq.gz,sample02_R2_001.fastq.gz

Step 2: Run VAPER

Note: This will use the default reference set. You can provide your own reference set using the --refs parameter.

nextflow run DOH-JDJ0303/VAPER \
    -r main \
    -profile <docker/singularity/.../institute> \
    --input samplesheet.csv \
    --outdir results \
    --max_cpus 8 \
    --max_memory 16.GB

Acknowledgements

VAPER would not be possible without the following people:
Holly Halstead (WA PHL) (check out her tool varcraft!)
Pauline Trinh (WA MEP)
Allison Black (WA MEP)
Stephanie Lunn (WA MEP)
Kristen Waterman (WA PHL)