Run folder sizes and Disk Space on the MiSeq

All run folder sizes listed below should be used only as an approximation.

• Folder size will vary depending on the raw cluster density and the number of clusters passing filter for the run.

• The examples below are based on dual-indexing runs with optimal clustering and clusters passing filter greater than 80%. The following also include FASTQ files generated on the instrument by MiSeq Reporter or Local Run Manager.

MiSeq v2 Chemistry
Kit Type	Read Length	Reagent Kit Configuration	Output Folder Size in GB
v2 50 cycle kits	2 x 25	Standard	14 - 16
v2 300 cycle kits	2 x 150	Standard	16 - 18
Micro	3 - 5
Nano	0.8 - 1.2
v2 500 cycle kits	2 x 250	Standard	22 - 24
Nano	1.6 - 1.8

MiSeq v3 Chemistry
Kit Type	Read Length	Reagent Kit Configuration	Output Folder Size in GB
v3 150 cycle kits	2 x 75	Standard	19 - 22
v3 600 cycle kits	2 x 300	Standard	22 - 26

Notes:

• The MiSeq hard drive is 700 GB total.

• 141 GB are partitioned to C:\ for Operating System Files and Illumina Software Installation.

• The remaining 559 GB are allocated for D:, where run data is stored, the following way:

  

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