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 can output the per-chromosome coverage

There is also mosdepth which is similar but also outputs the genome-wide coverage instead of just the per-chromosome coverage in a file named <prefix>.mosdepth.summary.txt

[Arton]

Thank you! It worked perfectly.

[Arton]

How do you calculate the total (genome-wide) average coverage from "samtools coverage" output which is per chromosome?

[cmdcolin]

you can try mosdepth. It outputs a file called <prefix>.mosdepth.summary.txt and the last line in it includes the genome wide mean/min/max coverages https://github.com/brentp/mosdepth (there are also various solutions in this thread Tools To Calculate Average Coverage For A Bam File? but i think a well tested tool for something like this is much preferred to the ad hoc scripts!)