omtools

Welcome to the omtools wiki!

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).