G400 fastq header description?

[Luke Nguyen]

Hello,

I am doing a comparison of duplicated reads on Illumina NovaSeq vs MGI G400 by checking the distribution of reads on the flowcell. I noticed the fastq header from the G400 is quite different from that of the NovaSeq.

For example, one of the headers is:

@F350009384L1C001R0010008170/1

which I interpret as "flowcell id: F350009384", "lane: L1", "tile column: C001", "tile row: R001", "read: /1" and the remaining part "0008170" is unclear to me. Could this be the X and Y coordinates of the cluster/DNB?

Would love to hear if my interpretation is correct. Thanks!

[GenoMax]

Complete genomics fastq header format has the following information:

• @<Flowcell-id><LaneNo><Column><Row><FieldofView></readNumber>
• Read1:
  • @F350009384 L1 C001 R001 00001290 /1
• Read2:
  • @F350009384 L1 C001 R001 00001266 /2

That said a recent basecalling software update from CG now has the ability of producing Illumina-like headers.

[Luke Nguyen]

Thank you everyone! MGI representatives told me the cluster/DNB location is not available in their fastq format. I would love to see if anyone used their new basecalling software as mentioned by GenoMax!