How to Calculate Average Coverage and Depth from ONT Sequencing

Question

[dheeraj]

Hello everyone,

I need to calculate the average coverage and average depth for an Oxford Nanopore (ONT) sequencing run. Is there any method, tool, or pipeline to calculate the average coverage and average depth of an ONT run?

Thank you

[lieven.sterck]

Hi,

what you done/tried already? Have you looked around to see what or how other people do this?

Do also include some more info to your question: which species, what kind of data, is there a reference genome available (or estimate of genome size)? ... Perhaps also indicate what you understand by coverage and/or depth (these are often used interchangeable and interpreted differently by people)

Very basically: you need to sum the total amount of bases sequenced (== produced by your sequencing run) and divide that by the total length of the genome.