SummonChimera infers integrated viral genomes with nucleotide precision from NGS data.

ABSTRACT:

Background

Viral integration into a host genome is defined by two chimeric junctions that join viral and host DNA. Recently, computational tools have been developed that utilize NGS data to detect chimeric junctions. These methods identify individual viral-host junctions but do not associate chimeric pairs as an integration event. Without knowing the chimeric boundaries of an integration, its genetic content cannot be determined.

Results

Summonchimera is a Perl program that associates chimera pairs to infer the complete viral genomic integration event to the nucleotide level within single or paired-end NGS data. SummonChimera integration prediction was verified on a set of single-end IonTorrent reads from a purified Salmonella bacterium with an integrated bacteriophage. Furt

SUBMITTER: Katz JP 

PROVIDER: S-EPMC4210586 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature