Add to the pipeline the new tool called f5c which is a reimplementation of Nanopolish and is much faster. Add this tool, but not replace nanopolish. Instead, make the pipeline run f5c or Nanopolish (or both) depending on user's desire, with something like: --nanopolish_fast5 <fast5 dir> to run with Nanopolish or --f5c_fast5 <fast5 dir> to run with f5c.
Finally, add a report for methylations with pycoMeth
Add to the pipeline the new tool called f5c which is a reimplementation of
Nanopolishand is much faster. Add this tool, but not replace nanopolish. Instead, make the pipeline runf5corNanopolish(or both) depending on user's desire, with something like:--nanopolish_fast5 <fast5 dir>to run withNanopolishor--f5c_fast5 <fast5 dir>to run with f5c.Finally, add a report for methylations with pycoMeth