How to calculate coverage of Nanopore long read data?
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12 weeks ago
Arton • 0

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.

sequencing coverage • 455 views
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12 weeks ago
cmdcolin ★ 2.9k

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

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Thank you! It worked perfectly.