Rapid Run vs. High Output mode in HiSeq 2500

[xiang.jiao]

Hi, we have been considering about using HiSeq 2500 to sequence ~100 cancer genomes. We were wondering why the Rapid Run mode saves so much time compared to the High Output mode (500 cycles in < 3 days versus 250 cycles in 6 days, if I understand correctly). Since the chemical procedure for each cycle seems to be quite similar in both mode (nucleotide incorporation -> wash -> imaging -> remove blocking and fluor group -> wash) and all reactions happen in a parallel manner, where comes the substantial difference in run time?

Many thanks in advance!

[AllSeq]

Hi, we have been considering about using HiSeq 2500 to sequence ~100 cancer genomes. We were wondering why the Rapid Run mode saves so much time compared to the High Output mode (500 cycles in < 3 days versus 250 cycles in 6 days, if I understand correctly). Since the chemical procedure for each cycle seems to be quite similar in both mode (nucleotide incorporation -> wash -> imaging -> remove blocking and fluor group -> wash) and all reactions happen in a parallel manner, where comes the substantial difference in run time?

Many thanks in advance!

Primarily from having a small surface area that gets imaged. The 'high output mode' flow cell has eight channels while the 'Rapid Run' flow cell has only two. There may be some other differences in the chemistry, but surface area (which translates to imaging time) is the biggest.

[xiang.jiao]

Thanks a lot AllSeq! That is exactly what we were looking for! By the way, do you how long the imaging time is for one channel?

[AllSeq]

No, I'm not sure of the specifics. Hopefully someone with a 2500 will chime in.

[HESmith]

The imaging time is ~10 minutes per cycle. Also, the chemistry and cycling parameters are different from the high-throughput mode.