TAR-VIR: a pipeline for TARgeted VIRal strain reconstruction from metagenomic data.

ABSTRACT:

Background

Strain-level RNA virus characterization is essential for developing prevention and treatment strategies. Viral metagenomic data, which can contain sequences of both known and novel viruses, provide new opportunities for characterizing RNA viruses. Although there are a number of pipelines for analyzing viruses in metagenomic data, they have different limitations. First, viruses that lack closely related reference genomes cannot be detected with high sensitivity. Second, strain-level analysis is usually missing.

Results

In this study, we developed a hybrid pipeline named TAR-VIR that reconstructs viral strains without relying on complete or high-quality reference genomes. It is optimized for identifying RNA viruses from metagenomic data by combining an effective rea

SUBMITTER: Chen J 

PROVIDER: S-EPMC6549370 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature