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.
Thank you! It worked perfectly.
How do you calculate the total (genome-wide) average coverage from "samtools coverage" output which is per chromosome?
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!)
Thank you! I eventually used the information generated by three tools (samtools coverage+ mosdepth + NanoPlot).