Question: What do Ns represent in a SPAdes assembly from single-end reads?
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gravatar for kcamnairb
6 months ago by
kcamnairb40
United States
kcamnairb40 wrote:

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

spades assembly • 248 views
ADD COMMENTlink modified 6 months ago by lieven.sterck2.4k • written 6 months ago by kcamnairb40

That could result from contig-formation/scaffolding.

ADD REPLYlink written 6 months ago by cschu1811.4k

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

ADD REPLYlink written 6 months ago by lieven.sterck2.4k

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

ADD REPLYlink written 6 months ago by kcamnairb40
1
gravatar for lieven.sterck
6 months ago by
lieven.sterck2.4k
Belgium, Ghent, VIB
lieven.sterck2.4k wrote:

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)

ADD COMMENTlink written 6 months ago by lieven.sterck2.4k
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