ViReMa : a virus recombination mapper of next-generation sequencing data characterizes diverse recombinant viral nucleic acids

作者：Stephanea Sotcheff, Yiyang Zhou, Jason Yeung, Yan Sun, John E. Johnson, Bruce E. Torbett, Andrew Routh · 发表于：GigaScience · 年份：2023 · DOI：10.1093/gigascience/giad009 · 被引用次数：32 · 研究领域：Evolution and Genetic Dynamics、Genomics and Phylogenetic Studies、Chromosomal and Genetic Variations

BACKGROUND: Genetic recombination is a tremendous source of intrahost diversity in viruses and is critical for their ability to rapidly adapt to new environments or fitness challenges. While viruses are routinely characterized using high-throughput sequencing techniques, characterizing the genetic products of recombination in next-generation sequencing data remains a challenge. Viral recombination events can be highly diverse and variable in nature, including simple duplications and deletions, or more complex events such as copy/snap-back recombination, intervirus or intersegment recombination, and insertions of host nucleic acids. Due to the variable mechanisms driving virus recombination and the different selection pressures acting on the progeny, recombination junctions rarely adhere to simple canonical sites or sequences. Furthermore, numerous different events may be present simultaneously in a viral population, yielding a complex mutational landscape. FINDINGS: We have previously developed an algorithm called ViReMa (Virus Recombination Mapper) that bootstraps the bowtie short-read aligner to capture and annotate a wide range of recombinant species found within virus populations. Here, we have updated ViReMa to provide an "error density" function designed to accurately detect recombination events in the longer reads now routinely generated by the Illumina platforms and provide output reports for multiple types of recombinant species using standardized formats. We demonst...