High-throughput bisulfite sequencing (NGS data analysis)

BiQ Analyzer HiMod Screenshot

BiQ Analyzer HiMod is the latest version of the popular interactive sequence analysis tool, designed for high-throughput targeted sequencing of 5-methylcytosine and its oxidized derivatives. BiQ HiMod facilitates processing and primary analysis of data obtained in standard targeted bisulfite sequencing experiments, as well as oxidative, Tet-assisted, chemical modification-assisted or formyl chemical modification-assisted bisulfite sequencing. The tool features substantially reworked graphical user interface, a number of new diagrams, and a new vector graphics engine.
Becker et al., NAR, 2014 | PDF
Lutsik et al., NAR, 2011 | PDF

Clonal bisulfite sequencing (Low complexity data analysis)

BiQ Analyzer Screenshot

"Classical" BiQ Analyzer is tool for a streamlined analysis of clonal bisulfite sequencing reads. With more than 3,000 downloads so far, BiQ Analyzer has become a standard tool for processing DNA methylation data from bisulfite sequencing. BiQ Analyzer has been selected by ABI to be part of the Applied Biosystems Software Community Program. This version comes with several GUI improvements but maintains full result compatibility with the previous versions.

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Bock et al., Bioinformatics, 2005 | PDF