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Bioinformatics Advance Access originally published online on September 1, 2005
Bioinformatics 2005 21(21):4067-4068; doi:10.1093/bioinformatics/bti652
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing

Christoph Bock 1,*, Sabine Reither 2, Thomas Mikeska 2, Martina Paulsen 2, Jörn Walter 2 and Thomas Lengauer 1

1Max-Planck-Institut für Informatik Saarbrücken, Germany
2Universität des Saarlandes FR 8.3 Biowissenschaften, Genetik/Epigenetik, Saarbrücken, Germany

*To whom correspondence should be addressed.

Summary: Manual processing of DNA methylation data from bisulfite sequencing is a tedious and error-prone task. Here we present an interactive software tool that provides start-to-end support for this process. In an easy-to-use manner, the tool helps the user to import the sequence files from the sequencer, to align them, to exclude or correct critical sequences, to document the experiment, to perform basic statistics and to produce publication-quality diagrams.

Emphasis is put on quality control: The program automatically assesses data quality and provides warnings and suggestions for dealing with critical sequences. The BiQ Analyzer program is implemented in the Java programming language and runs on any platform for which a recent Java virtual machine is available.

Availability: The program is available without charge for non-commercial users and can be downloaded from http://biq-analyzer.bioinf.mpi-inf.mpg.de/

Contact: cbock{at}mpi-inf.mpg.de

Received on June 9, 2005; revised on August 17, 2005; accepted on August 26, 2005

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