How to calculate coverage of Nanopore long read data?

Question

[Arton]

I have Nanopore long read data from several patients. I would like to calculate coverage of the long read data but I couldn't find any tool that does this. I did some calculations myself (SUM (samtools depth)/total bases) but I'm not sure if this is accurate. Any suggestion of tools or approaches to calculate the coverage for long read data would be appreciated.

Answer 1

[cmdcolin]

See samtools coverage http://www.htslib.org/doc/samtools-coverage.html

[Arton]

Thank you! It worked perfectly.