biq-analyzer.bioinf.mpi-inf.mpg.de

BiQ Analyzer - a software tool for DNA methylation analysis

BiQ Analyzer is a software tool for easy visualization and quality control of DNA methylation data from bisulfite sequencing.

Highlights:


  • End-to-end support of the analysis process: from raw sequence files to a comprehensive documentation and visualization
  • Automatically generate publication-quality lollipop diagrams (show example)
  • Integrated 1-click multiple sequence alignment
  • Automated CpG highlighting- never spend your time highlighting CpGs by hand anymore
  • Open electropherogram files to check for sequencing problems (requires an electropherogram viewer such as Chromas LITE)
  • Generate MethDB-compatible DNA methylation files for database submission
  • Factor 5 speedup of sequence analysis while at the same time achieving better data quality

Intended users:


  • Anyone who works with DNA methylation data from bisulfite sequencing
  • Occasional users as well as experts (the former will benefit from the help that the program gives in order to achieve a good quality management whereas the latter will save hours and days of tedious work)

Details on methodology

See our Applications Note that appeared in Bioinformatics (Oxford University Press).


A few more reasons to use BiQ Analyzer:


How to proceed from here:

If you consider using BiQ Analyzer, we strongly suggest that you proceed as follows (this should not take more than 30 minutes and it might save you a lot of time later on):

  1. Step through the Guided Tour / Exemplary Analysis, where we show commented sceenshots of an examplary analysis.
  2. Download and install the program as described in the Installation section
  3. Reproduce the analysis from the Guided Tour yourself, using the demonstration data that we provide. This is the fastest way to understand how the program works and how it can be used to speed up data analysis.
  4. Apply it to your own dataset!
  5. Look into the FAQ in case there is any unexpected behavior of the program.
  6. If you have any problems or suggestions, please write an e-mail to biq-analyzer@bioproject.de.

Typical screenshot of BiQ Analyzer in action:

Please see References on how to cite BiQ Analyzer