Question: What do Ns represent in a SPAdes assembly from single-end reads?
0
gravatar for kcamnairb
3.0 years 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 • 807 views
ADD COMMENTlink modified 3.0 years ago by lieven.sterck10k • written 3.0 years ago by kcamnairb40

That could result from contig-formation/scaffolding.

ADD REPLYlink written 3.0 years ago by cschu1812.6k

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

ADD REPLYlink written 3.0 years ago by lieven.sterck10k

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 3.0 years ago by kcamnairb40
1
gravatar for lieven.sterck
3.0 years ago by
lieven.sterck10k
VIB, Ghent, Belgium
lieven.sterck10k 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 3.0 years ago by lieven.sterck10k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2450 users visited in the last hour
_