Comparative evaluation of SNVs, indels, and structural variations detected with short- and long-read sequencing data.

ABSTRACT: Short- and long-read sequencing technologies are routinely used to detect DNA variants, including SNVs, indels, and structural variations (SVs). However, the differences in the quality and quantity of variants detected between short- and long-read data are not fully understood. In this study, we comprehensively evaluated the variant calling performance of short- and long-read-based SNV, indel, and SV detection algorithms (6 for SNVs, 12 for indels, and 13 for SVs) using a novel evaluation framework incorporating manual visual inspection. The results showed that indel-insertion calls greater than 10 bp were poorly detected by short-read-based detection algorithms compared to long-read-based algorithms; however, the recall and precision of SNV and indel-deletion detection were similar betwee

SUBMITTER: Kosugi S 

PROVIDER: S-EPMC11024196 | biostudies-literature | 2024 Apr

REPOSITORIES: biostudies-literature