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Bismark Summary Reports

Please Note: This script has now been incorporate into Bismark, see the bismark documentation for reference. Also note that MultiQC (http://multiqc.info) performs much the same task as well as supporting other tools.

Bismark is a tool used for aligning Bisfulfite-Sequencing libraries, giving information about DNA methylation.

For every sample that is analysed, Bismark produces statistics such as alignment rates and methylation calls. A report is generated to show this data, fantastic for interrogating single samples. It is of less use when a large number of samples are processed in parallel, however (as is increasingly the norm).

This script takes a list of bismark-processed BAM files as an input, looks for the corresponding bismark reports and produces a HTML summary report. The report is interactive, allowing the data to be plotted with absolute counts or percentages. Methylation calls can be shown in CpG, CHG and CHH context.

In addition to the HTML report, a text file is generated with tab delimited numbers for post-processing.

Example Output

Bismark Coverage Curves Plot See the full example report here: bismark_summary_report.html

You can also see the tab-delimted text file here: bismark_summary_report.txt


perl bismark_summary_report.pl *.bam


This script is run on the command line. There are currently no customisation options.


The script is written in Perl and run on the command line.


Theis script was written for use at the National Genomics Infrastructure at SciLifeLab in Stockholm, Sweden. They are part of a larger repository of NGI Visualization Scripts.

For more information, please get in touch with Phil Ewels.