UMI-Gen: A UMI-based read simulator for variant calling evaluation in paired-end sequencing NGS libraries.

ABSTRACT:

Motivation

With Next Generation Sequencing becoming more affordable every year, NGS technologies asserted themselves as the fastest and most reliable way to detect Single Nucleotide Variants (SNV) and Copy Number Variations (CNV) in cancer patients. These technologies can be used to sequence DNA at very high depths thus allowing to detect abnormalities in tumor cells with very low frequencies. Multiple variant callers are publicly available and are usually efficient at calling out variants. However, when frequencies begin to drop under 1%, the specificity of these tools suffers greatly as true variants at very low frequencies can be easily confused with sequencing or PCR artifacts. The recent use of Unique Molecular Identifiers (UMI) in NGS experiments has offered a way to accurate

SUBMITTER: Sater V 

PROVIDER: S-EPMC7484502 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature