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:

For any feedback or questions regarding this article (Illumina Knowledge Article #6711), contact Illumina Technical Support techsupport@illumina.com.

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