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Good coverage value for de novo assembly with NanoPore Reads?
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13 months ago

Hello, I am trying to do a de-novo assembly of a turtle genome of about 2.15 gbases with Nanopore Minion reads. I have read about Canu as a good tool for this purpose, but it seems it yields good a good assembly with reads of at least 20x coverage, and the coverage of my reads is only about 2.5x. Is this value too low for de novo assembly with Nanopore reads? What would be a good coverage value?

Thank you everyone

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Entering edit mode
13 months ago
colindaven ♦ 1.3k
Hannover Medical School

Yes, 2.5X is too low for de novo.

For structural variant detection vs a reference genome about 10X is recommended.

For de novo I would suggest 30-40X, whereby the longest reads are the most important.

Sorry, but 2.5 X is likely only maybe useful for somehow scaffolding Illumina contigs if you have them (difficult, poor results expected).

You can print the read distribution eg by using stats.sh from bbmap so we can have a look if you like.

The tool Miniasm or wtdbg2 https://github.com/ruanjue/wtdbg2 might give you a very very sketchy assembly but I doubt it.

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