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



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.



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.



kevinyip@cse.cuhk.edu.hk and tf.chan@cuhk.edu.hk



Supplementary data are available at Bioinformatics online.
School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
Alden King-Yung
AK
Leung
Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China.
Tsz-Piu
TP
Kwok
School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
Raymond
R
Wan
School of Biomedical Engineering, Science and Health System, Drexel University, Philadelphia, PA, USA.
Ming
M
Xiao
Institute for Human Genetics.|Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.
Pui-Yan
PY
Kwok
Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China.|Hong Kong Bioinformatics Centre.
Kevin Y
KY
Yip
School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China|Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China.|Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.|Hong Kong Bioinformatics Centre.
Ting-Fung
TF
Chan
D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D016678:Genome; D023281:Genomics / Q000379:methods; D006801:Humans; D056972:Optical Restriction Mapping / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software