splitting big paired fastq files

[JahnDavik]

Hi there,
I do my 'bioinformatic' work in CLC. Now I sit with many (30) large files with paired end reads (~10GB each direction) and my computer is stalling if I'd try to use all in a de novo assembly. Hence, I am looking for a tool to split the files in, say, 4.
I am afraid I am not familiar with the linux world. So, I am lookiing for scripts (R preferably, or Perl) that would solve this?

Thank you.
jd

[swbarnes2]

If you split your fastq, you aren't going to get a good assembly. You really want a computer with more memory, so it can handle the whole fatq.

If you really need to split it, use unix built-in programs.

split -l 40000000 myfastq.fq

should split it into separate files, each with 40,000,000 lines, or 10 million reads.

[JahnDavik]

Thank you for your prompt reply!
There are 150-200 mill reads in each of the paired fastq files and I just expected that to be quite redundant.