Approximate sizes of sequencing run output folders

Background

The run folder sizes listed in this article are only an approximation based on dual-indexed runs with optimal cluster densities for each platform. For runs on nonpatterned flow cells, the size approximation is based on runs with clusters passing filter greater than 80%.

The actual size will vary depending on the raw cluster density and the number of clusters passing filter for each run.

Additional run folder size considerations:

• iSeq 100, MiniSeq and 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 either the MiSeq Reporter FASTQ workflow or the Local Run Manager FASTQ workflow (MiSeq Control Software 3.1 and higher).

• NextSeq 1000/2000 folder sizes include local analysis output, which can add another 25-120+ GB depending on workflow.

• NovaSeq 6000 folders do not include FASTQ files as part of the total output folder size as no onboard analysis is available for this platform.

• The output folder size in the tables below is reported in Gigabytes (GB), except for the NovaSeq X which is reported in Terabytes (TB).

Illumina recommends storing the output folder for iSeq 100, NextSeq 500/550, and NextSeq 1000/2000 runs on a network location. NovaSeq 6000 and NovaSeq X Series Control Software requires storing the output folder on a network location.

iSeq 100

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

MiniSeq

Mid Output

Read Length	Output Folder Size in GB
2 x 150	2.3 - 2.6

High Output

Read Length	Output Folder Size in GB
2 x 150	7.0 - 8.0
2 x 75	6.0 - 8.0
1 x 75	2.0 - 4.0

Rapid

Read Length	Output Folder Size in GB
1 x 100	2

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	3.0 - 5.0
2 x 150	Nano	0.8 - 1.2
2 x 25	Standard	14 - 16

MiSeq i100 Series

See Knowledge Article Estimating Disk Space Utilization on the MiSeq i100 Series

NextSeq 500/550

Mid Output

Read Length	Output Folder Size in GB
2 x 150	62 - 66
2 x 75	39 - 46

High Output

Read Length	Output Folder Size in GB
2 x 150	160 - 170
2 x 75	92 - 97
1 x 75	50 - 78

NextSeq 1000/2000 (Standard and XLEAP runs are expected to have similar sizes)

P1

Read Length	Output Folder Size in GB
2 x 300	85-95
2 x 150	50 - 55
2 x 101	40 - 45
2 x 75	35 - 40

P2

Read Length	Output Folder Size in GB
2 x 300	140-160
2 x 150	89 - 99
2 x 101	65 - 66
2 x 75	44 - 55

P3

Read Length	Output Folder Size in GB
2 x 150	165 - 170
2 x 101	103 - 126

P4 (XLEAP Only)

Read Length	Output Folder Size in GB
2 x 150	170 - 180
2 x 100	100 - 130
2 x 50	70 - 80
1 x 50	40 - 50

NovaSeq 6000

SP

Read Length	Output Folder Size in GB
1 x 36	20
2 x 150	185
2 x 250	400

S1

Read Length	Output Folder Size in GB
2 x 150	370

S2

Read Length	Output Folder Size in GB
2 x 150	730

S4

Read Length	Output Folder Size in GB
1 x 36	240
2 x 150	2190

NovaSeq X Series

Values listed below are PER FLOW cell in Terabytes (TB).

1.5B

Read Length	cBCL Only in TB	BCL Convert (GZIP) in TB	BCL Convert (ORA) in TB
2 x 50	0.054 - 0.091	0.132 - 0.221	0.086 - 0.143
2 x 100	0.106 - 0.181	0.265 - 0.442	0.173 - 0.286
2 x 150	0.163 - 0.272	0.397- 0.662	0.259 - 0.429

10B

Read Length	cBCL Only in TB	BCL Convert (GZIP) in TB	BCL Convert (ORA) in TB
2 x 50	0.34 - 0.57	0.83 - 1.38	0.54 - 0.89
2 x 100	0.68 - 1.13	1.65 - 2.76	1.08 - 1.79
2 x 150	1.02 - 1.70	2.48 - 4.14	1.62 - 2.68

25B

Read Length	cBCL Only in TB	BCL Convert (GZIP) in TB	BCL Convert (ORA) in TB
2 x 50	0.85 - 1.42	2.07 - 3.45	1.35 - 2.23
2 x 100	1.70 - 2.83	4.13 - 6.90	2.70 - 4.47
2 x 150	2.55 - 4.25	6.200 - 10.35	4.05 - 6.70

DRAGEN Analysis files can ADD the following additional data in terabytes (TB) to the expected Output folder size based on Analysis options selected. Approximate file sizes are based on a single flow cell, 2x150 cycle sequencing run.

Flow Cell Type	BAM (TB)	CRAM (TB)	GVCF+VCF (TB)
1.5B	0.4	0.1	<0.1
10B	2.5	1.0	0.2
25B	6.3	2.5	0.5

For any feedback or questions regarding this article (Illumina Knowledge Article #1508), contact Illumina Technical Support [email protected].