Approximate sizes of sequencing run output folders

07/27/21


The run folder sizes listed in this bulletin should be used only as an approximation. Folder size will vary depending on the raw cluster density and the number of clusters passing filter. Folder sizes are based on runs with optimal cluster densities for each platform and dual indexing. For runs on nonpatterned flow cells, the size approximations are based on runs with pass filter greater than 80%.

 

Additional run folder size considerations:

  • iSeq 100 folder sizes include FASTQ files generated by the Local Run Manager FASTQ workflow.
  • MiniSeq, NextSeq 500/550 (NextSeq Control Software v4.0 and higher) folder sizes include FASTQ files generated by the Local Run Manager FASTQ workflow.
  • MiSeq folder sizes include FASTQ files generated by the MiSeq Reporter FASTQ workflow and MiSeq (MiSeq Control Software 3.1 and higher) Local Run Manager FASTQ workflow.
  • NextSeq 1000/2000 folder sizes include local analysis output, which can add another 25–120+ GB depending on workflow.
  • HiSeq 1500/2500, HiSeq 3000/4000, HiSeq X, and NovaSeq 6000 folders do not include FASTQ files as part of the total output folder size. Folder sizes for HiSeq 1500/2500, HiSeq 3000/4000, HiSeq X, and NovaSeq 6000 are representative of a single flow cell.

Illumina recommends storing the output folder for iSeq 100, NextSeq 500/550, NextSeq 1000/2000, HiSeq 1500/2500, HiSeq 3000/4000, and HiSeq X runs on a network location. NovaSeq Control Software requires the output folder to be stored on a network location.

 

iSeq 100 | MiniSeq | MiSeq | NextSeq 500/550 | NextSeq 1000/2000 | HiSeq 1000/1500/2000/2500 | HiSeq 3000/4000 | HiSeq X | NovaSeq 6000

 

 

iSeq 100

Read Length Output Folder Size in GB
2 x 150 1.5 - 2.5

 

 

MiniSeq

Read Length Output Folder Size in GB
Mid Output High Output Rapid
2 x 150 2.3 - 2.6 7 - 8 N/A
2 x 75 N/A 6 - 8 N/A
1 x 100 N/A N/A 2
1 x 75 N/A 2 - 4 N/A

 

 

MiSeq

v3 Chemistry
Read Length Output Folder Size in GB
2 x 300 22 - 26
2 x 75 19 - 22

 

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

 

 

NextSeq 500/550

Read Length Output Folder Size in GB
Mid Output High Output
2 x 150 62 - 66 160 - 170
2 x 75 39 - 46 92 - 97
1 x 75 N/A 50 - 78

 

 

NextSeq 1000/2000

Read Length Output Folder Size in GB
P2 P3
2 x 150 150 500
2 x 101 100 300
2 x 50 75 150
2 x 25 N/A 100

*The size of the folder depends on the analysis (onboard vs. cloud) and the analysis configuration. Values listed reflect local analysis runs, which consume the most disk space.

 

 

HiSeq 1000/1500/2000/2500

Read Length High Output TruSeq SBS v3
Output Folder Size in GB
High Output SBS v4
Output Folder Size in GB
HiSeq Rapid Run v2
Output Folder Size in GB
2 x 250 N/A N/A 80 - 100
2 x 125 295 - 310 190 - 210 N/A
2 x 100 225 N/A 55 - 60
2 x 50 133 77 - 83 32 - 36

 

 

HiSeq 3000/4000

Read Length Output Folder Size in GB
2 x 150 560
2 x 75 290
2 x 25 80

 

 

HiSeq X

Read Length Output Folder Size in GB
2 x 150 560

 

 

NovaSeq

Read Length SP Flow Cell
Output Folder Size in GB
S1 Flow Cell
Output Folder Size in GB
S2 Flow Cell
Output Folder Size in GB
S4 Flow Cell
Output Folder Size in GB
1 x 35 N/A N/A N/A 280 - 350
2 x 50 65 - 80 134 - 167 333 - 417 N/A
2 x 100 134 - 167 266 - 333 667 - 833 1600 - 2000
2 x 150 200 - 250 400 - 500 1000 - 1250 2400 - 3000
2 x 250 325 - 400 N/A N/A N/A