length of N's in abyss-scaffolds.fa

Question

[xiaofeiwang198266]

Dear there,

I see this thread https://groups.google.com/forum/#!msg/abyss-users/8E5609CSrUY/1NkZIDO6rx0J about the N's in assembly, which is associated with my question.

I see NCBI can accept gapped format of assembly now. So, I want to double check 2 things about "N's" in ABySS assembly output of "abyss-scaffolds.fa". First, no matter how long the gap is, what does N represent for, is it for gap/unknown_base not ambiguous base(s), right? I know it might be difficult to define these two. Second, if the length of N's is equal to the gap length exactly (I assume it is)?

Thank you so much!

Best,
Xiaofei

[xiaofeiwang198266]

Hi ABySS community,

Here it is (in bolded-italic format below) how did I answered the question for WGS submission. Could you please help me double check it based on the ABySS output? Thanks!

Is every N in your sequence within a gap, created by you or the assembly program to combine the sequences into scaffolds?

• Yes, every N is within a gap
• No, some of the N's are in gaps, but there are also N's that represent one or a few ambiguous base calls
• No, none of the N's represents a gap. There are only a few scattered Ns in the sequence, and they are ambiguous base calls

Minimum number of N's in a row that represents a gap of estimated length

Do any of the N's represent gaps of completely unknown size?

• Yes
• No, all gaps are of estimated size (even if a particular size was used for small gaps (eg, 10 N's))