Detect the Illumina sequencer model

Extract the Illumina sequencer instrument information from a FASTQ file.

Instrument codes

The Illumina instrument type can generally be determined from a FASTQ header based on these identifier codes:

FASTQ header

Simply run this command in the shell:

gunzip -c S1_R1_001.fastq.gz | head -n 1

Here’s an example output:

@NB501431:435:HGK55BGX3:2:11101:13079:1046 1:N:0:1

Note that BGX3 here indicates that the FASTQ was generated by a NextSeq sequencer.