Difference between variants called in sequences with 2-channel SBS and 4-channel SBS

Question

[Shin Taguchi]

Hi all.

I have been using 4-channel SBS for sample sequencing and am considering using 2-channel SBS in the future.

I would like to know if there are any papers that discuss the differences in SNPs obtained between 4-channel SBS and 2-channel SBS.

Thank you.

Answer 1

[GenoMax]

I am not sure if you are going to find a publication that compares identical samples analyzed via 4 and 2 channel chemistries. It has been Illumina's official position that sequence generated from any of its chemistries/sequencers should be equivalent. We have compared RNAseq samples for the two chemistries in past and the concordance was excellent.

You may end up having to do some validation yourself if you have a lot of previous data that you need to combine with the new chemistry to be absolutely sure.

[Shin Taguchi]

Thank you for your reply.

Your comment is very helpful.