Sequencing on the MiSeq i100 can be up to 50% cheaper per base than its predecessor. Sequencing run times are also shorter (less than one day). The new MiSeq uses a different chemistry (XLEAP), so there will be a different error rate and bias between the new and old machines. You should therefore plan to complete studies using one or the other, or perform bridging experiments to control for the different chemistries.
Flowcell naming is more straightforward on the Miseq i100:
- 5 M = up to 5 Milion reads. Available in 300 and 600 cycle kits.
- 25 M = up to 10 Million reads. Available in 100, 300, 600 and 1000 cycle kits.
- 50 M = up to 50 Million reads. Available in 100, 300 and 600 cycle kits.
- 100 M = up to 100 Million reads. Available in 100 and 300 cycle kits.
For more detailed specs on the instrument, please see Illumina's website: MiSeq i100 specifications