NGSEP3: accurate variant calling across species and sequencing protocols.

ABSTRACT:

Motivation

Accurate detection, genotyping and downstream analysis of genomic variants from high-throughput sequencing data are fundamental features in modern production pipelines for genetic-based diagnosis in medicine or genomic selection in plant and animal breeding. Our research group maintains the Next-Generation Sequencing Experience Platform (NGSEP) as a precise, efficient and easy-to-use software solution for these features.

Results

Understanding that incorrect alignments around short tandem repeats are an important source of genotyping errors, we implemented in NGSEP new algorithms for realignment and haplotype clustering of reads spanning indels and short tandem repeats. We performed extensive benchmark experiments comparing NGSEP to state-of-the-art software using

SUBMITTER: Tello D 

PROVIDER: S-EPMC6853766 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature