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:
- 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?
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!