Coverage summary

[dfornika]

Generate a depth-of-coverage summary for each isolate, including:

• Configurable depth threshold
• Percent of genome that are below the depth threshold
• .bed file showing low-coverage regions

...and possibly also

• A .pdf plot of depth of coverage across the genome

[dfornika]

It would probably make sense to tie the depth threshold to our existing min_depth parameter:

https://github.com/BCCDC-PHL/tbprofiler-nf/blob/f87175235b642d48cd03db5908b67c7902761037/nextflow.config#L21

[dfornika]

A couple of tools that might be useful:

https://github.com/brentp/mosdepth

https://telatin.github.io/bamtocov

[taranewman]

This tool looks like it can produce a .bed file showing only low-coverage regions: https://github.com/telatin/covtobed

[dfornika]

Fixed by #13 and #14