Measurement error and variant-calling in deep Illumina sequencing of HIV.

ABSTRACT:

Motivation

Next-generation deep sequencing of viral genomes, particularly on the Illumina platform, is increasingly applied in HIV research. Yet, there is no standard protocol or method used by the research community to account for measurement errors that arise during sample preparation and sequencing. Correctly calling high and low-frequency variants while controlling for erroneous variants is an important precursor to downstream interpretation, such as studying the emergence of HIV drug-resistance mutations, which in turn has clinical applications and can improve patient care.

Results

We developed a new variant-calling pipeline, hivmmer, for Illumina sequences from HIV viral genomes. First, we validated hivmmer by comparing it to other variant-calling pipelines on real HIV

SUBMITTER: Howison M 

PROVIDER: S-EPMC7963075 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature