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Old 02-12-2016, 09:03 AM   #1
terdon
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Location: Athens

Join Date: Feb 2016
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Default How can I validate fastq files?

I want to check my fastq files to make sure that:
  • The two files of a paired reads run have the same size and number of sequences.
  • That each sequence in a fastq file has a corresponding quality line with the same number of characters.
  • That a fastq file is correctly formatted, basically that it consists of groups of 4 lines.
  • That it ends with a new line, that it isn't truncated.
Now, it's relatively simple to whip up a little script to check all this but I would expect there are already dedicated tools for this sort of thing and would rather not reinvent the wheel.

I am aware of fastqc but it doesn't seem to validate the format of the files themselves, only the quality of the sequence they describe.

So, is there any tool designed for validating fastq files?
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Old 02-12-2016, 09:47 AM   #2
GenoMax
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If you only want to validate the files then you could use this: http://genome.sph.umich.edu/wiki/FastQValidator

Is there a reason why you think the files may be mangled in some way?
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