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Instrument washes required for Illumina sequencing platforms

Many different factors contribute to a successful sequencing run. One important aspect is to make sure that the fluidics lines are thoroughly flushed between sequencing runs to prevent any salt accumulation. It is also important that the fluidics systems are well maintained when the instrument is idle.
With the introduction of the newer Illumina sequencing platforms, instrument washes are not necessary for iSeq 100 and NextSeq 1000/2000 systems. The new sequencing cartridges contain pumps, valves, and all other fluidics for the system, which are discarded after a run.
This bulletin outlines the types of washes required, the time needed to complete the wash, and how frequently the respective washes should be performed for all Illumina sequencing instruments.
Note: Water and other chemicals used should be lab grade.
MiSeq system
Type of wash
Description
Reagents to prepare
Approximate time
Frequency
Manual post-run wash
Standard instrument wash performed between sequencing runs
0.5% Tween 20 wash solution
20 minutes
Perform after every run
Manual post-run wash including template line wash
Post-run wash with user-supplied NaOCl to flush the template line
0.5% Tween 20% and 0.01% NaOCl wash solution
30 minutes
Perform as needed (for VeriSeq PGS runs, wash is performed after every run)
Manual maintenance wash
The wash includes a series of three wash steps that thoroughly flush the system
0.5% Tween 20 wash solution
90 minutes
Perform every 30 days
Manual standby wash
Two consecutive washes that flush each position to remove any remaining reagents or salt accumulation
0.5% Tween 20 wash solution
2 hours
Perform to prepare for idle mode (system unused for seven days), and every 30 days if the instrument remains idle
Instructions for performing the wash procedures can be found in the MiSeq System Guide.
MiniSeq and NextSeq 500/550 systems
Type of wash
Description
Reagents to prepare
Approximate time
Frequency
Automatic post-run wash
When sequencing is complete, the software initiates an automatic post-run wash using the wash solution and NaOCl provided in the reagent cartridge
Not applicable
60 minutes
Automatic after every run
Manual quick wash
The wash flushes the system with user-supplied Tween 20 wash solution
0.05% Tween 20 wash solution
20 minutes
Required every 14 days (instrument idle with cartridges in place)
Required every seven days (instrument is in a dry state with cartridges removed or in Array Mode for NextSeq550)
Required after a shutdown
Manual post-run wash
The wash flushes the system with user-supplied NaOCl and Tween 20 wash solution
0.05% Tween 20% and 0.12% NaOCl solution
90 minutes
Required if the automatic post-run wash was not performed
Instructions for performing the wash procedures can be found in the MiniSeq System Guide, NextSeq 500 System Guide, or NextSeq 550 System Guide.
HiSeq 1500/2000/2500 Systems (all manual washes)
Type of wash
Description
Reagents to prepare
Approximate time
Frequency
Water wash
(8 SBS positions)
Required after each sequencing run to wash the system and check fluidics
Laboratory-grade water
20 minutes
Perform after every run
If the instrument has been idle for one day or more, perform before beginning a new sequencing run
Water wash
(8 SBS and 10 paired-end positions)
Required after each sequencing run to wash the system and check fluidics
Recommended for sequencing runs that include an indexing read or are paired end
Laboratory-grade water
60 minutes
Perform after every run
If the instrument has been idle for one day or more, perform before beginning a new sequencing run
Water wash
(8 SBS, 10 paired-end positions, and 1 template loading position)
Required after each rapid run mode sequencing run to wash the system and check fluidics
Laboratory-grade water
10 minutes
Perform after every run
If the instrument has been idle for one day or more, perform before beginning a new sequencing run
Maintenance wash
Two types of workflows:
(1) Tween 20 and ProClin 300, or
(2) Tween 20 only (if ProClin solution is not available)
Either workflow will require a subsequent water wash if the instrument is going to be idle for more than five days
Workflow 1
0.5% Tween 20 wash solution and 0.03% ProClin 300 solution
Workflow 2 0.5% Tween 20 wash solution | 130 minutes (for High Output mode), 60 minutes (for Rapid mode) | Perform every 10 days, optionally after a run | | Maintenance wash (Switching from High Output to Rapid Run mode) | Requires performing a Rapid Mode maintenance wash (assuming that the maintenance wash in High Output mode has already been performed) Two types of workflows: (1) Tween 20 and ProClin 300, or (2) Tween 20 only (if ProClin solution is not available) Either workflow will require a subsequent water wash if the instrument is going to be idle for more than five days | Workflow 1 0.5% Tween 20 wash solution and 0.03% ProClin 300 solution Workflow 2 0.5% Tween 20 wash solution | 60 minutes | Perform when switching modes from High Output to Rapid Run | | Maintenance wash (Switching from Rapid Run to High Output mode) | Requires performing a Rapid Mode maintenance wash followed by a maintenance wash in High Output mode Two types of workflows: (1) Tween 20 and ProClin 300, or (2) Tween 20 only (if ProClin solution is not available) Either workflow will require a subsequent water wash if the instrument is going to be idle for more than five days | Workflow 1 0.5% Tween 20 wash solution and 0.03% ProClin 300 solution Workflow 2 0.5% Tween 20 wash solution | 60 minutes + 130 minutes = 190 minutes | Perform when switching modes from Rapid Run to High Output |
Instructions for performing the wash procedures can be found in the respective system guides here: HiSeq 1500, HiSeq 2000, HiSeq 2500.
HiSeq 3000/4000/X systems (all manual washes)
Type of wash
Description
Reagents to prepare
Approximate time
Frequency
Water wash
(8 SBS positions)
Required after each sequencing run to wash the system and check fluidics
Laboratory-grade water
20 minutes
Perform after every run
If the instrument has been idle for one day or more, perform before beginning a new sequencing run
Water wash
(8 SBS and 10 paired-end positions)
Required after each sequencing run to wash the system and check fluidics
Recommended for sequencing run that includes an indexing read or paired end
Laboratory-grade water
60 minutes
Perform after every run
If the instrument has been idle for one day or more, perform before beginning a new sequencing run
Maintenance wash
Two types of workflows:
(1) Tween 20 and ProClin 300, or
(2) Tween 20 only (if ProClin solution is not available)
Either workflow will require a subsequent water wash if the instrument is going to be idle for more than five days
Workflow 1
0.5% Tween 20 wash solution and 0.03% ProClin 300 solution
Workflow 2
0.5% Tween 20 wash solution
90 minutes
Perform every 10 days, optionally after a run
Instructions for performing the wash procedures can be found in the respective system guides here: HiSeq 3000, HiSeq 4000, HiSeq X.
cBot 2 System (all manual washes)
Type of wash
Description
Reagents to prepare
Approximate time
Frequency
Pre-run and post-run water wash
Perform an instrument wash before and after each run to clear salts and enzymes from the instrument hardware and to prevent clogs
Laboratory-grade water
Between each run and if the instrument is idle for more than one day
Maintenance wash
Perform wash to remove traces of reagents from internal cBot components and inhibit the growth of microorganisms
5% DECON or 100 mM NaOH (if DECON is not available)
Perform once per month
Instructions for performing the wash procedures can be found in the cBot 2 System Guide.
NovaSeq 6000 systems
Type of wash
Description
Reagents to prepare
Approximate time
Frequency
Automatic post-run wash
When the sequencing run is complete, the software initiates an automatic post-run wash using the wash solution and NaOCl provided in the reagent cartridge
Not applicable
80 minutes
Automatic after every run
Manual maintenance wash
The wash flushes the system with user-supplied NaOCl and Tween 20 wash solution
0.05% Tween 20 wash solution and 0.25% NaOCl
80 minutes
Perform this wash when there has not been a four-lane run with a post-run wash, no maintenance wash has been performed within the last 14 days, or when a post-run wash fails or is incomplete.
Instructions for performing the wash procedure can be found in the NovaSeq 6000 System Guide.
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