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A software tool for the alignment of both single molecule restriction maps (Rmaps) and in silico restriction maps of sequence contigs to a reference. Maligner provides two modes of alignment: an efficient, sensitive dynamic programming implementation that scales to large eukaryotic genomes, and a faster indexed based implementation for finding alignments with unmatched sites in the reference but not the query. We compare our software to other publicly available tools on Rmap datasets and show that Maligner finds more correct alignments in comparable runtime.


Identifies large structural variations (SVs) from kilobases to more than a hundred kilobases. OMSV is a comprehensive SV calling pipeline and corresponding open-source software. It combines optical maps and sequencing data to detects precise SV break points and uncover novel sequences involved in the SVs. OMSV outperformed the publicly available tool for SV detection from OM data in three aspects, namely (i) OMSV identified many more SVs at a precision level similar to this method, (ii) OMSV identified many of the complex SVs but this method missed all of them, (iii) OMSV ran much faster by not requiring a time-consuming de novo assembly of the optical maps.

OMACC / Optical-Map-Assisted Contig Connector

Closes the gaps between scaffolded contigs with a higher accuracy compared with a similar tool. OMACC is advantageous because it takes into account gap size carefully via rescaling optical map and applying length constraint on selecting the path of contigs for gap closure. In addition, it applies an advanced graph search algorithm to efficiently infer the correct number of repeat copies in the gap between two contigs. We apply OMACC and FINISH on both simulated and real data sets. OMACC achieves a >90% accuracy, higher than the <73% by FINISH, and more than doubles the contig N50 lengths. OMACC also maintains a similar sensitivity as FINISH does. Thus, OMACC should benefit various downstream biological studies via accurately connecting contigs into a more complete genome with the assistance of optical map.