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Optical mapping software tools

Optical mapping is a technique for capturing fluorescent signal patterns of long DNAmolecules (in the range of 0.1 Mbp to 1 Mbp). Recently, it has been complementing the widely-used short-read sequencing technology by assisting with scaffolding and…
OMBlast
Desktop

OMBlast

A fast alignment method aimed at aligning high-throughput optical maps while…

A fast alignment method aimed at aligning high-throughput optical maps while preserving overall alignment precision and recall. The underlying algorithm of OMBlast is a seed-and-extend method, where…

Maligner
Desktop

Maligner

A software tool for the alignment of both single molecule restriction maps…

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…

runBNG
Desktop

runBNG

Allows to run BioNano tasks on Linux clusters. runBNG provides the same…

Allows to run BioNano tasks on Linux clusters. runBNG provides the same functions that are implemented in BioNano IrysView. The software enables analysis such as quality control of single molecule…

OMSV
Desktop

OMSV

Identifies large structural variations (SVs) from kilobases to more than a…

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…

OMTools
Desktop

OMTools

Provides filtering tools on optical mapping data such as filtering by size or…

Provides filtering tools on optical mapping data such as filtering by size or number of signals. OMTools is a software package which comprises modules for visualization (OMView), processing optical…

OMWare
Desktop

OMWare

A tool for efficient assembly of genome-wide physical maps. OMWare efficiently…

A tool for efficient assembly of genome-wide physical maps. OMWare efficiently generated 405 de novo map assemblies of a single datasets collected from the cotton species Gossypium raimondii. The…

BioNanoAnalyst
Desktop

BioNanoAnalyst

Provides a computational method for assessment of the quality of reference…

Provides a computational method for assessment of the quality of reference assemblies using BioNano data. BioNanoAnalyst is a package that offers a visual representation of the assembly using…

Irys Extract
Desktop

Irys Extract

Creates genomic information from data collected by the BioNano Genomics Irys…

Creates genomic information from data collected by the BioNano Genomics Irys platform. Irys Extract provides molecule images and genome aligned intensity profiles based on the automated analysis of…

OMSim
Desktop

OMSim

Produces synthetic optical map data which mimics real Bionano Genomics data.…

Produces synthetic optical map data which mimics real Bionano Genomics data. OMSim is based on statistical models in which the parameters were derived from real data. It helps user to select the…

G T A T C G C T A
misSEQuel
Desktop

misSEQuel

Enhances the quality of draft genomes by identifying misassembly errors and…

Enhances the quality of draft genomes by identifying misassembly errors and their breakpoints using paired-end sequence reads and optical mapping data. misSEQuel also fulfills the critical need for…

MapLinker
Desktop

MapLinker

Reduces markedly the human effort required to integrate information from…

Reduces markedly the human effort required to integrate information from physical maps and whole-genome shotgun (WGS) assembly. MapLinker allows users to manipulate and save the data output. It also…

Twin
Desktop

Twin

An index-based method for aligning in silico digested contigs to an optical…

An index-based method for aligning in silico digested contigs to an optical map. Our results demonstrate that Twin is an order of magnitude faster than competing methods on the largest genome. Most…

IRYSVIEW
Desktop

IRYSVIEW

Allows to visualize and analyze the next generation mapping data produced by…

Allows to visualize and analyze the next generation mapping data produced by the Irys Instrument.

SOMA
Web
Desktop

SOMA Scaffolding using Optical Map Alignment

Automatically place genomic sequences on an optical restriction map. The…

Automatically place genomic sequences on an optical restriction map. The techniques used in SOMA were specifically designed with the characteristics of short-read sequencing in mind and have been…

G T A T C G C T A
OMACC
Desktop

OMACC Optical-Map-Assisted Contig Connector

Closes the gaps between scaffolded contigs with a higher accuracy compared with…

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…

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