OMBlast: alignment tool for optical mapping using a seed-and-extend approach.

ABSTRACT:

Background

Optical mapping is a technique for capturing fluorescent signal patterns of long DNA molecules (in the range of 0.1–1 Mbp). Recently, it has been complementing the widely used short-read sequencing technology by assisting with scaffolding and detecting large and complex structural variations (SVs). Here, we introduce a fast, robust and accurate tool called OMBlast for aligning optical maps, the set of signal locations on the molecules generated from optical mapping. Our method is based on the seed-and-extend approach from sequence alignment, with modifications specific to optical mapping.

Results

Experiments with both synthetic and our real data demonstrate that OMBlast has higher accuracy and faster mapping speed than existing alignment methods. Our tool also sho

SUBMITTER: Leung AK 

PROVIDER: S-EPMC5409310 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature