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@FelixKrueger FelixKrueger released this 26 Apr 15:23
· 446 commits to master since this release

bismark_methylation_extractor

  • The methylation extractor now creates output directories if they don't exist already.

  • The options --ample_mem and --buffer_size <string> are now mutually exclusive.

  • Changed the directory being passed on when --cytosine_report is specified from parent directory' to 'output directory'.

bismark2report

  • Major rewrite of bismark2report: HTML file are now rendered using Plotly.js [plotly.js v1.39.4] which is completely open source and free to use. Highcharts and JQuery were dropped, as was raised here: #177.
    The files bioinfo.logo, bismark.logo, plot.ly and plotly_template.tpl are read in dynamically from a new folder plotly. bismark_sitrep and all its contents no longer ship with Bismark. The Bismark HTML reports should be completely self-contained, here is an example paired-end Bismark report.

bismark2summary

  • Major rewrite of bismark2summary: HTML file are now rendered using Plotly.js [plotly.js v1.39.4] which is completely open source and free to use. Highcharts and JQuery were dropped, as was raised here: #177. The files bioinfo.logo, bismark.logo, plot.ly and plotly_template.tpl are read in dynamically from a new folder plotly. bismark_sitrep and all its contents no longer ship with Bismark. The Bismark HTML Summary reports should be completely self-contained, here is an example of a percent alignment plot for a single cell experiment:
    Alignment Summary Report scBS-seq.

And finally, here are some examples for a WGBS summary report, an RRBS report (no deduplication), and the full scBS-seq report and scBS-seq data file.