Dataset Information
OMBlast: alignment tool for optical mapping using a seed-and-extend approach.
Ontology highlight
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 shows significant improvement when aligning data with SVs.Availability and implementation
OMBlast is implemented for Java 1.7 and is released under a GPL license. OMBlast can be downloaded from https://github.com/aldenleung/OMBlast and run directly on machines equipped with a Java virtual machine.Contact
kevinyip@cse.cuhk.edu.hk and tf.chan@cuhk.edu.hkSupplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Leung AK
PROVIDER: S-EPMC5409310 | biostudies-literature | 2017 Feb
REPOSITORIES: biostudies-literature
Publications
OMBlast: alignment tool for optical mapping using a seed-and-extend approach.
Bioinformatics (Oxford, England) 20170201 3
<h4>Background</h4>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 ...[more]
