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Old 04-14-2013, 10:39 PM   #1
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Location: Norway

Join Date: Aug 2012
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Default 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.
JahnDavik is offline   Reply With Quote
Old 04-14-2013, 10:59 PM   #2
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Location: San Diego

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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.
swbarnes2 is offline   Reply With Quote
Old 04-14-2013, 11:16 PM   #3
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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.
JahnDavik is offline   Reply With Quote

big file, clc bio, fastq, splitting

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