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  • splitting big paired fastq files

    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

  • #2
    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.

    Code:
    split -l 40000000 myfastq.fq
    should split it into separate files, each with 40,000,000 lines, or 10 million reads.

    Comment


    • #3
      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.

      Comment

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