Step 4: Demultiplexing (NextSeq 1000/2000 Sequencing v2.1)

This step is a semiautomated step.

The integration starts the step automatically and demultiplexing data from the GenerateFASTQ secondary analysis is parsed back to Clarity LIMS. The lab scientist reviews the demultiplexing result parsed into Clarity LIMS, assigns QC flags, and completes the step.

Do not add samples to the Ice Bucket or start or complete the step. The integration does this action automatically.

The following automations are configured on the step:

• Assign Demultiplexing QC flags—Automatically assigns QC flags based on the criteria set on the step fields.
• Set Next Step—Automatically sets the next step to Advance and the samples complete the protocol.

The following table lists the 12 master step fields that are configured on the Demultiplexing (NextSeq 1000/2000 Sequencing v2.1) master step.

Master Step Field Configuration for Demultiplexing (NextSeq 1000/2000 Sequencing v2.1) Step

Field Name

Field Type

Field Constraints/Options

Preset Values/Additional Options and Drop-Down Items

Criteria 1 - Source Data Field

Text Dropdown
• Required: No
• Read Only: No
• Custom Entries: Yes
• # Reads
• # Perfect Index Reads
• # One Mismatch Index Reads
• # of >= Q30 Bases (PF)

Criteria 2 - Source Data Field

Text Dropdown
• Required: No
• Read Only: No
• Custom Entries: Yes
• # Reads
• # Perfect Index Reads
• # One Mismatch Index Reads
• # of >= Q30 Bases (PF)

Criteria 1 - Operator

Text Dropdown
• Required: No
• Read Only: No
• Custom Entries: Yes
• >=
• <=
• =
• !=

Criteria 2 - Operator

Text Dropdown
• Required: No
• Read Only: No
• Custom Entries: Yes
• >=
• <=
• =
• !=

Criteria 1 - Threshold Value

Numeric
• Required: No
• Read Only: No
• Valid integer value

Criteria 2 - Threshold Value

Numeric
• Required: No
• Read Only: No
• Valid integer value

Log

Multiline Text
• Required: No
• Read Only: Yes

Not applicable

Analysis Completed Time

Text
• Required: No
• Read Only: Yes

Hidden

Do not delete / modify. These actions will break the integration.

 

Analysis Started Time

Text
• Required: No
• Read Only: Yes

Hidden

Do not delete / modify. These actions will break the integration.

Analysis Status

Text
• Required: No
• Read Only: Yes

Hidden

Do not delete / modify. These actions will break the integration.

BSSH Analysis ID

Text
• Required: No
• Read Only: Yes

Hidden

Do not delete / modify. These actions will break the integration.

Reagent Cartridge ID

Text
• Required: No
• Read Only: Yes
• Hidden
• Used for parsing demultiplexing results

Do not delete / modify. These actions will break the integration.

There are five fields defined on the Demultiplexing (NextSeq 1000/2000 Sequencing v2.1) step. The fields are used to display the demultiplexing result metrics for individual library in the sample pool.

The following table lists the global fields that are configured on the Demultiplexing (NextSeq 1000/2000 Sequencing v2.1) step.

Global Field Configuration for Demultiplexing (NextSeq 1000/2000 Sequencing v2.1) Step

Field Name

Field Type

Field Constraints/Options

# of >= Q30 Bases (PF)

Numeric
• Required: No
• Read Only: Yes

# One Mismatch Index Reads

Numeric
• Required: No
• Read Only: Yes

# Perfect Index Reads

Numeric
• Required: No
• Read Only: Yes

# Reads

Numeric
• Required: No
• Read Only: Yes

Mean Quality Score (PF)

Numeric
• Required: No
• Read Only: Yes

Refer to NextSeq 1000/2000 Integration v2.2 Validation and Troubleshooting for details.