Product detail

ViruSpy: a pipeline for viral identification from metagenomic samples

ZILE, K. KUPKOVÁ, K. CANTALUPO, P. ELLISON, M. WALDMAN, J. GLICKMAN, C. BUSBY, B.

Product type

software

Abstract

ViruSpy is a pipeline designed for virus discovery from metagenomic sequencing data available in NCBI’s SRA database. The first step identifies viral reads in the metagenomic sample with Magic-BLAST, which allows this step without needing to download the (often quite large) metagenomic dataset. The extracted raw reads are assembled into contigs using MEGAHIT and annotated for genes by Glimmer and for conserved domains by RPS-tBLASTn. Following annotation, the Building Up Domains (BUD) algorithm allows us to tell whether the viral genomes are non-native (i.e. integrated) to a host genome.

Keywords

metagenome, virus

Create date

27. 9. 2017

Location

https://github.com/NCBI-Hackathons/ViruSpy

Possibilities of use

Využití výsledku jiným subjektem je možné bez nabytí licence (výsledek není licencován)

Licence fee

Poskytovatel licence na výsledek nepožaduje licenční poplatek

www

https://github.com/NCBI-Hackathons/ViruSpy