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What do Ns represent in a SPAdes assembly from single-end reads?

The fungal genome assembly I've done using SPAdes with single-end reads has stretches of Ns present. I would expect this with paired end reads but I'm not sure what they represent when the assembly is done with single-end reads. The spades options I used were --iontorrent and --careful. Do these N's represent ambiguous bubbles in the assembly or spots where there are mixed bases in the reads?

Thanks, Brian

assembly spades
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updated by lieven.sterck lieven.sterck • written by kcamnairb • kcamnairb

That could result from contig-formation/scaffolding.

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written by cschu181 cschu181

Do you have many of them and/or long stretches?

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written by lieven.sterck lieven.sterck

There are 8 stretches of Ns in the assembly. Some of them are up to 512 bp, which is longer than the read length.

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written by kcamnairb • kcamnairb

1 answer

Yes, those Ns will represent ambigous base calls in the reads that the assembly part could not resolve. Non-resolvable bubbles will either be arbitrary popped or result in broken contigs (not 100% sure what SPAdes will do with them)

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written by lieven.sterck lieven.sterck

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