Oxford Nanopore and Coverage

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4.8 years ago

AP ▴ 100

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 • 6.2k views

ADD COMMENT • link 4.8 years ago by AP ▴ 100

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Do you have this data?

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

ADD REPLY • link 4.8 years ago by Joe 21k

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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 REPLY • link 4.8 years ago by AP ▴ 100

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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 REPLY • link 4.8 years ago by GenoMax 147k

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

ADD REPLY • link 4.8 years ago by AP ▴ 100

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