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


BACKGROUND
The program is available without charge for non-commercial users and can be downloaded from http://biq-analyzer.bioinf.mpi-inf.mpg.de/
Bock
Christoph
C
Max-Planck-Institut für Informatik Saarbrücken, Germany. cbock@mpi-inf.mpg.de
Reither
Sabine
S
Mikeska
Thomas
T
Paulsen
Martina
M
Walter
Jörn
J
Lengauer
Thomas
T
D004247:DNA / Q000032:analysis* / Q000737:chemistry*; D019175:DNA Methylation; D016133:Polymerase Chain Reaction / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods* / Q000592:standards; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000592:standards; D012984:Software; D013447:Sulfites / Q000737:chemistry*; D014584:User-Computer Interface
D013447:Sulfites; D004247:DNA