bismark2report uses a Bismark alignment report to generate a graphical HTML report page. Optionally, further reports of the Bismark suite such as deduplication, methylation extractor splitting or M-bias reports can be specified as well. If several Bismark reports are found in the same folder, a separate report will be generated for each of these, whereby the output filename will be derived from the Bismark alignment report file. Bismark2report attempts to find optional reports automatically based on the file basename.
Parent program: bismark
Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. Its main features are: (1) bisulfite mapping and methylation calling in one single step; (2) Supports single-end and paired-end read alignment; (3) Supports ungapped and gapped alignments (4) Alignment seed length, number of mismatches etc. are adjustable (5) Output discriminates between cytosine methylation in CpG, CHG and CHH context