Systematic comparison of variant calling pipelines of target genome sequencing cross multiple next-generation sequencers.

ABSTRACT: Targeted genomic sequencing (TS) greatly benefits precision oncology by rapidly detecting genetic variations with better accuracy and sensitivity owing to its high sequencing depth. Multiple sequencing platforms and variant calling tools are available for TS, making it excruciating for researchers to choose. Therefore, benchmarking study across different platforms and pipelines available for TS is imperative. In this study, we performed a TS of Reference OncoSpan FFPE (HD832) sample enriched by TSO500 panel using four commercially available sequencers, and analyzed the output 50 datasets using five commonly-used bioinformatics pipelines. We systematically investigated the sequencing quality and variant detection sensitivity, expecting to provide optimal recommendations for future research.

SUBMITTER: Feng B 

PROVIDER: S-EPMC10794554 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature