break scaffolds with many Ns to contigs

[yzzhang]

Dear all,
Recently I sequenced a plant genome using Hiseq 2000, 101bp paired end reads. I assembled the reads to contigs. Because I just sequenced one insert libray (size 400 bp), I got so many contigs. To build a better genome and get more genes, I aligned the contigs to a related species genome using ABACAS, and filled the gaps using Gapfiller. Maybe the two species have some different regions in chromosomes, so in the result there are many Ns in the generated scaffolds (the same as the chromosomes number). So I want to break the scaffolds to contigs if there are more than 100 Ns between two continuous sequences. Because I am only a biologist and with on knowledge on scripts. Could anyone could indicate me which software or script works for my data? Many thanks.
Best Wishes,
yun

[westerman]

There are probably many ways. Using fastx toolkit plus unix should work. I think, but have not tried, the following

1) fasta_formatter to convert the contigs into single-line sequences
2) sed -e 's/N{100,}/>/g'
3) fastx_renamer
4) (optional) fasta_formatter for more sensible line breaks

A short perl/python/ruby program would also work but that would require some level of programming.

What I gave above is just the bare-bones -- the idea -- and not the actual implementation which is left up to you.

[yzzhang]

Thank you very much. Finally I got a perl script for this purpose. I need to learn some programming skills, I am wondering perl or python is earier to learn, and try perl first. Anyway, Thanks.

There are probably many ways. Using fastx toolkit plus unix should work. I think, but have not tried, the following

1) fasta_formatter to convert the contigs into single-line sequences
2) sed -e 's/N{100,}/>/g'
3) fastx_renamer
4) (optional) fasta_formatter for more sensible line breaks

A short perl/python/ruby program would also work but that would require some level of programming.

What I gave above is just the bare-bones -- the idea -- and not the actual implementation which is left up to you.