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

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,...

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Bibliographic Details
Published in:Bioinformatics 2005-11, Vol.21 (21), p.4067-4068
Main Authors: Bock, Christoph, Reither, Sabine, Mikeska, Thomas, Paulsen, Martina, Walter, Jörn, Lengauer, Thomas
Format: Article
Language:English
Subjects:
Biological and medical sciences
DNA - analysis
DNA - chemistry
DNA Methylation
Fundamental and applied biological sciences. Psychology
General aspects
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Polymerase Chain Reaction - methods
Sequence Alignment - methods
Sequence Alignment - standards
Sequence Analysis, DNA - methods
Sequence Analysis, DNA - standards
Software
Sulfites - chemistry
User-Computer Interface
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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@mpi-inf.mpg.de
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/bti652