Is there a specification anywhere for how a Nanopore FASTQ header should be formatted?

I am creating strategies for generating test FASTQ files and would like to ensure I am generating "correct" nanopore sequence identifiers.

  • $\begingroup$ Could you clarify? Do you want to simulate ONT reads and make sure the headers are realistic? Or do you have actual reads and want to understand what information the actual headers encode? Or something else? $\endgroup$ Oct 25, 2019 at 13:02
  • $\begingroup$ @DanielStandage see updated question $\endgroup$ Oct 26, 2019 at 3:57
  • $\begingroup$ Thanks. I think that improves the question a lot! $\endgroup$ Oct 28, 2019 at 13:34
  • $\begingroup$ Are you just looking for FASTQ format spec? en.wikipedia.org/wiki/FASTQ_format#Format $\endgroup$
    – TimD1
    Dec 9, 2021 at 15:36

1 Answer 1


The headers are defined by the basecaller (guppy, Albacore, bonito, etc) during basecalling. They have changed many times over the years, but generally they start with a readID of @+UUIDv4 followed by multiple entries separated by spaces, of form key=value

For example:

@945da76d-b7ef-4c65-91a1-e69c85832185 runid=2cf9e7c4dd1888d9a1090ebc394dd5b7cb2fe3f0 read=126 ch=181 start_time=2017-10-17T06:43:19Z barcode=barcode01

This is still valid, however, there is some movement to add sam tags to parse data through to sam files when aligned.


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