HPViewer: sensitive and specific genotyping of human papillomavirus in metagenomic DNA.

ABSTRACT:

Motivation

Shotgun DNA sequencing provides sensitive detection of all 182 HPV types in tissue and body fluid. However, existing computational methods either produce false positives misidentifying HPV types due to shared sequences among HPV, human and prokaryotes, or produce false negative since they identify HPV by assembled contigs requiring large abundant of HPV reads.

Results

We designed HPViewer with two custom HPV reference databases masking simple repeats and homology sequences respectively and one homology distance matrix to hybridize these two databases. It directly identified HPV from short DNA reads rather than assembled contigs. Using 100 100 simulated samples, we revealed that HPViewer was robust for samples containing either high or low number of HPV reads. Usin

SUBMITTER: Hao Y 

PROVIDER: S-EPMC6658710 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature