How to identify fastq source - Illumina or ONT?

Question

[ChillarAnand]

There are lot of publicly available sample fastq files.

How to identify if they are generated from Illumina machines or ONT(Oxford Nanopore Technology) machines or any other machines?

Answer 1

[GenoMax]

Assuming the data has not been modified in any way, you could look for a couple of things

• Length of read (majority of reads)
  Illumina : 300 bp or less (while 600 bp reads are possible no one generally does that)
  

  Nanopore : Reads that are generally longer than 300 bp

• Fastq headers
  

  Illumina header format is well defined - https://en.wikipedia.org/wiki/FASTQ_format#Illumina_sequence_identifiers
  

  ONT headers look like

    @3cfgt6cd-3671-4tgd-c61g-0c759bt068d0 runid=eb6214851489c8e00eb0dcbd00d737f7cccxxxx read=2178 ch=232 start_time=2021-11-21T10:35:44Z

• Quality scores
  

  Illumina reads - scores are going to be closer to Q35+
  

  Nanopore reads - scores are going to be generally lower