<p>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 <code>@+UUIDv4</code> followed by multiple entries separated by spaces, of form key=value</p>
<p>For example:</p>
<pre><code>@945da76d-b7ef-4c65-91a1-e69c85832185 runid=2cf9e7c4dd1888d9a1090ebc394dd5b7cb2fe3f0 read=126 ch=181 start_time=2017-10-17T06:43:19Z barcode=barcode01
</code></pre>
<p>This is still valid, however, there is some movement to add sam tags to parse data through to sam files when aligned.</p>

CC BY-SA 4.0
2021-12-09T03:25:34.087Z
2021-12-09T03:25:34.087Z
PsyFer
<p>Is there a specification anywhere for how a Nanopore FASTQ header should be formatted?   </p>

<p>I am creating <a href="https://lab41.github.io/hypothesis-bio/api/fastq.html" rel="nofollow noreferrer">strategies for generating test FASTQ files</a> and would like to ensure I am generating "correct" nanopore <a href="https://lab41.github.io/hypothesis-bio/api/sequence_identifiers.html" rel="nofollow noreferrer">sequence identifiers</a>.</p>

CC BY-SA 4.0
2019-10-25T13:02:31.017Z
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?
Daniel Standage
CC BY-SA 4.0
2019-10-26T03:57:15.040Z
@DanielStandage see updated question
Michael Hall
CC BY-SA 4.0
2019-10-28T13:34:12.953Z
Thanks. I think that improves the question a lot!
Daniel Standage
CC BY-SA 4.0
2021-12-09T15:36:00.557Z
Are you just looking for FASTQ format spec? https://en.wikipedia.org/wiki/FASTQ_format#Format
TimD1
<nanopore><fastq>
Nanopore FASTQ header specifications
# Nanopore FASTQ header specifications

(Asked by: username_0 on 2019-10-19)

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

I am creating [strategies for generating test FASTQ files](https://lab41.github.io/hypothesis-bio/api/fastq.html) and would like to ensure I am generating "correct" nanopore [sequence identifiers](https://lab41.github.io/hypothesis-bio/api/sequence_identifiers.html).

**Tags:** nanopore, fastq
> **Comments:**
> **username_1**: 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?  
> **username_0**: @DanielStandage see updated question  
> **username_1**: Thanks. I think that improves the question a lot!  
> **username_2**: Are you just looking for FASTQ format spec? https://en.wikipedia.org/wiki/FASTQ_format#Format  

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## 1 answers

### Answer by username_3 on 2021-12-09. Score: 3

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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