split fastq sequence by motif (string of Ns)

Question

[adhb]

I have a fairly long (800 kbp) consensus fastq that I want to split at each string of Ns (arbitrarily, let's say 3 or more Ns), depositing each of the sequence (non-N) strings into a new file (together, not separate files) and omitting the strings of Ns.

I've done a bunch of searching trying to find a lead on how to tackle this, but maybe I'm not phrasing the question correctly.

Thanks.

Answer 1

[h.mon]

Ask for the advice of the search sages:

https://github.com/MadsAlbertsen/miscperlscripts/blob/master/split.scaffolds.to.contigs.pl

http://seqanswers.com/forums/showthread.php?t=12993

http://seqanswers.com/forums/showthread.php?t=27035

When you google, it is not only the keywords that matter (by the way I used break contigs n), it is about respecting and revering the sages.