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Old 08-06-2019, 08:21 AM   #3
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Location: New England

Join Date: Jun 2012
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The number of reads (molecules sequenced, also called clusters) is determined by the concentration of library added. There is an optimal number the sequencing center will be aiming for depending on the type of library you have.

The length of the reads is determined by the kit you decide to use. If you have an insert between your Illumina adapters of 600 bp, you could use a 600 cycle kit and read 300 bp in each direction. You could not use a 600 cycle kit with an insert size of 50 bp, since you would be reading far past the end of your insert into the Illumina adapter and flow cell.

The amount of time a MiSeq run takes is dependent on the length of the reads. Library hydridization and cluster formation takes a couple of hours. After that each read (cycle) takes around 5 minutes. So a 4 hour run is likely just 2x25 bp. A 55 hour run would be the full 300x300 bp run. The cost of the run is dependent on how many cycles you want performed - 2x25 bp kits contain less reagents and are cheaper than 2x300 bp kits.
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