RNA-seq accuracy and reproducibility for the mapping and quantification of influenza defective viral genomes.

ABSTRACT: Like most RNA viruses, influenza viruses generate defective viral genomes (DVGs) with large internal deletions during replication. There is accumulating evidence supporting a biological relevance of such DVGs. However, further understanding of the molecular mechanisms that underlie the production and biological activity of DVGs is conditioned upon the sensitivity and accuracy of detection methods, that is, next-generation sequencing (NGS) technologies and related bioinformatics algorithms. Although many algorithms were developed, their sensitivity and reproducibility were mostly assessed on simulated data. Here, we introduce DG-seq, a time-efficient pipeline for DVG detection and quantification, and a set of biological controls to assess the performance of not only our bioinformatics algor

SUBMITTER: Boussier J 

PROVIDER: S-EPMC7668258 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature