Convert abyss scaffolds to contigs

Question

[jm440]

Hi all,

I assembled a genome using paired end reads and abyss assembler with the following command:

abyss-pe k=128 in='R1.fq R2.fq'

I got a scaffold file, which I then filtered based on several criteria. I now want to get an updated contig file from this scaffold file. My strategy is to split the scaffolds into new lines based on the occurrence of 'N' similar to what is shown in this post: How to get contigs from scaffolds

I have two concerns though:

1. I noticed in the scaffold file that there are also lower case Ns ("n") that appear (pretty rarely) in some scaffolds, see below for snippet from one of the scaffolds. What are these and is it safe to ignore these when splitting by "N"s?

Example:

>5050  
...GATCACTTAGGCCAAAAGCAGGnAAAGAAGGCAAATCTGC...

2.Should I be splitting to contigs by a certain minimum # of "N"s or is 1 or more Ns the correct way to do this?

Thanks a bunch for any tips!

Answer 1

[h.mon]

I am not very familiar with ABySS, but I am almost sure it should output a contigs file and a scaffolds file.

In any case, don't break the scaffolds at Ns, use the AGP file to correctly identify and break the scaffolds into contigs. See ABySS file formats and the NCBI AGP specification.

[jm440]

Yes ABySS does output a contig file along with a scaffold file, however I then filtered out scaffolds from the scaffold file using several criteria and so I want to produce an updated contig file based on this new scaffold file. Hopefully that makes sense..

I will check out AGP files - thank you!