Question: Oxford Nanopore and Coverage
0
gravatar for AP
7 weeks ago by
AP90
AP90 wrote:

Hello,

I was wondering if anyone knew how to calculate the coverage of a specific genome using output metrics from Oxford Nanopore Technology.

For instance, can anyone calculate coverage information using the total number of pores ran, the N50, and the data in Gb? Information of the expected genome size would be known.

Any help on this would be appreciated.

Thanks!

oxford nanopore coverage • 140 views
ADD COMMENTlink written 7 weeks ago by AP90

Do you have this data?

Why not simply remap the reads and calculate the coverage 'properly'?

ADD REPLYlink written 7 weeks ago by Joe16k

Yes absolutely. But I was hoping to be able to have a rough estimate without using a bioinformatics pipeline (similar to what can be done with Illumina technology).

ADD REPLYlink written 7 weeks ago by AP90
1

If by coverage you simply mean total nucleotides sequenced/size of genome = x coverage then you can calculate that. Have you tried NanoPlot (https://github.com/wdecoster/NanoPlot )?

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by genomax80k

Thank you very much, this is quite useful. I haven't used NanoPlot but will take a look.

ADD REPLYlink written 7 weeks ago by AP90
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