VirusSeeker: a new computational tool for eukaryotic virus discovery and composition analysis

While the bacterial microbiome is become increasingly recognized for its role in health and disease, the virome has been less well studied, even though studies have shown that viruses are part of the normal human microbial flora and can modulate host immune response to pathogenic viruses and have been linked to diseases such as inflammatory bowel disease and acquired immunodeficiency syndrome (AIDS). Bioinformatic tools can easily evaluate the bacterial microbiome in Next Generation Sequencing (NGS) datasets by utilizing single, universally shared and phylogenetically informative genes such as the bacterial 16S ribosomal RNA genes.  In contrast, virus detection in NGS data using bioinformatics tools relies on aligning viral sequences to virus reference databases, which can be limited in accuracy due to the intrinsic rapid mutation rate of viruses. 
 
VirusSeeker is a new open source NGS data analysis pipeline that can perform novel virus discovery and evaluate virome composition1. VirusSeeker rapidly identifies candidate viral sequences by comparing NGS reads with virus-only databases, minimizing the number of sequences aligned compared to larger comprehensive databases. False positive identifications are reduced by the use of sequential BLAST pipelines and the use of a curated virus databases. A number of studies have demonstrated the effectiveness of VirusSeeker in detecting multiple highly divergent RNA and DNA viruses from different families2,3,4.
 
Please contact the CIIID Bioinformatics Core for more information on using VirusSeeker to probe your NGS dataset for virome discovery and composition.
 
References:

1. Zhao et al., Virology. 503(2017) 21-30.
2. Lim et al., Nat Med. 21 (2015) 1228-1234.
3. Handley et al., Cell Host Microbe 19 (2016) 323-335.
4. Monaco, et al., Cell Host Microbe 19 (2016) 311-322.