Instrument codes

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

• AAXX: Genome Analyzer
• BCXX: HiSeq v1.5
• ACXX: HiSeq High-Output v3
• ANXX: HiSeq High-Output v4
• ADXX: HiSeq RR v1
• AMXX, BCXX: HiSeq RR v2
• ALXX: HiSeqX
• BGXX, AGXX: High-Output NextSeq
• AFXX: Mid-Output NextSeq
• 5 letter/number: MiSeq

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.

References

• HBC wiki
• Biostars post #1
• Biostars post #2
• DFCI Core instrument list