Interactive data analysis in bisulphite DNA sequencing

Sequencing of bisulphite-modified DNA is a widely-used method for analysis of genomic methylation. Although straightforward in principle, a number of technical problems with sequencing and data analysis can impede progress.

CpGviewer aims to be a simple integrated tool for handling bisulphite sequencing projects. It can process plain text sequences or a variety of electropherogram formats, and allows interactive editing of the sequences, aligned to a reference sequence.

The primary and secondary CpGviewer editing windows look like this:

CpGviewer interactive grid

CpGviewer also offers the facility to design primers for bisulphite-treated templates and to output figures for publication, like this one:

CpGviewer output diagram

(Click to display the image at full size.)

Documentation and download

The User Guide (PDF) explains in detail all the capabilities of CpGviewer.

You can also download the current version of CpGviewer bundled with the User Guide.


CpGviewer was written by Ian Carr. It runs on Microsoft Windows, using the .NET framework.

Carr IM, Valleley EMA, Cordery SF, Markham AF & Bonthron DT (2007). Sequence analysis and editing for bisulphite genomic sequencing projects. Nucleic Acids Res., 35:e79. Or: PDF version (11 MB).