omtools

Welcome to the omtools wiki!

Major visualization modes in OMView. Five types of views are available to visualize optical mapping data for different purposes: (A) Regional view, (B) Anchor view, (C) Alignment view, (D) Multiple alignments view and (E) Molecule view

https://pmc.ncbi.nlm.nih.gov/articles/PMC5870549/

Optical mapping

Optical mapping is a technique for imaging DNA molecules along which specific labels are captured. These labels form distinct patterns along DNA molecules based on their nucleotide sequences. Compared with the short read length in next-generation sequencing (∼150 bp), DNA molecules in optical mapping data are several orders longer, at ∼100–1000 kb (Lam et al., 2012). Because of the much greater read length, optical mapping has been used for assisted scaffolding, (Dong et al., 2013), structural variations detection (Cao et al., 2014, Mak et al., 2016) and microbial strain typing (Schwan et al., 2010). There are currently two instrument platforms available for generating optical mapping data: OpGen Inc. and BioNano Genomics Inc. Emerging computational methods have been developed for data analysis. To gain knowledge and insights from the optical mapping data, human analysis and interpretation is required and usually involves data visualization. At present, three visualization tools for optical mapping are available: BioNumerics v7 (Applied Maths NV), IrysView (Shelton et al., 2015) and JBrowse (Skinner et al., 2009). However, none of them could provide multiple visualization styles in accordance to the types of application. Here, we present the software package OMTools, which comprises modules for visualization (OMView), processing optical mapping data and alignment results, and simulation. The package has fast loading time, easy installation and support to multiple data formats (Supplementary Tables S1 and S2).

Руководство OMTools v1.4

https://barionleg.github.io/omtools/OMToolsManual_uR.pdf

https://en.wikipedia.org/wiki/Radiological_information_system

https://en.wikipedia.org/wiki/Picture_archiving_and_communication_system

1.0

https://barionleg.github.io/omtools/OpticalMapFileSpecification_1.pdf

1.4

https://barionleg.github.io/omtools/OpticalMapFileSpecification.pdf

https://barionleg.github.io/omtools/OMToolsManual.pdf

OMTools

A software package for optical mapping data processing, analysis and visualization

Please refer to "OMToolsManual.pdf" for more details.

Quick steps

1. Compile the OMTools package in the OMTools folder: javac -d bin -sourcepath src -cp "lib/*" @classes
2. Build a runnable jar file for OMTools: jar cvfm OMTools.jar manifest -C bin .
3. Run OMTools: java -jar OMTools.jar

Basic steps

You may refer to the wiki page to check how to use OMTools, particularly for the latest DLE-1 data.

Issues

In case other users have the same problems in using OMTools, please report the potential issues on the Issues page. We will answer you ASAP.

Publications

1. Leung, Alden King-Yung, et al. "OMBlast: alignment tool for optical mapping using a seed-and-extend approach." Bioinformatics (2017).

2. Leung, Alden King-Yung, et al. "OMTools: a software package for visualizing and processing optical mapping data." Bioinformatics (2017).