Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data.

ABSTRACT:

Background

Accurate detection of polymorphisms with a next generation sequencer data is an important element of current genetic analysis. However, there is still no detection pipeline that is completely reliable.

Result

We demonstrate two new detection methods of polymorphisms focusing on the Polymorphic Edge (PED). In the matching between two homologous sequences, the first mismatched base to appear is the SNP, or the edge of the structural variation. The first method is based on k-mers from short reads and detects polymorphic edges with k-mers for which there is no match between target and control, making it possible to detect SNPs by direct comparison of short-reads in two datasets (target and control) without a reference genome sequence. The second method is based on bid

SUBMITTER: Miyao A 

PROVIDER: S-EPMC6599308 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature