Asymmetric sequencing on Illumina Novaseq S4 beyond specification | Cycle Transferring

[dugong]

Hello,

I would like to sequence 250 bases on `Illumina Novaseq S4`, on read 2.

1) Kits of illumina come in the following sizes: https://emea.illumina.com/systems/se...fications.html

2) You can setup the sequencer for asymmetric sequencing, so that from a standard paired-end 2*100bp kit reads `150` bases from R1, and only `50` of the R2 (or vice versa).

3) On `SP` kit they now support `2 x 250 bp`, but not on `S4`.

4) On the (largest) `S4`, the longest kit is `2*150`. It would be theoretically possible to sequence `250 + 50`. Or if that's too much, `200 + 100` is okay too.


The read quality at 150 bases is excellent, so I expect at least 200 useful bases.


- Did anyone tried this, or could point me to relevant information?
- I read q82817 and q59603
- Can you even specify such strong asymmetry in the software?
- Very importantly: Are there any risk of losing the lane?
- Are there any other risks (other than quality issues beyond 150 bases, which i assume I can easily trim away)?


Thanks so much for your time!

ps. originally posted on biology.stackexchange-112881, but it might be the wrong audience.

[GSeq94]

Hi, I am not an expert at all and wouldn't be able to tell you much about the quality after 150 bp, but we have been doing some sequencing from snRNAseq from 10X Genomics on the NovaSeq6000. The reads here are R1 28 and R2 90 bp, the asymmetry is not as pronounced as in your case, but an S1 200cycles copes well with it and our costumers are happy with the data.

[amikelov]

Hi dugong!

I very curious if you managed to get the answer or tried this kind of asymmetric sequencing (beyond specification) yourself. Is there anyone update on the topic?

Thanks!