ViruSpy: a pipeline for viral identification from metagenomic samples

ViruSpy: a pipeline for viral identification from metagenomic samples

Software

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.

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.

metagenome, virus

metagenome, virus

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

Use of the result by another entity is possible without acquiring a license (the result is not licensed)

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