Per-lane Loading

Multiple Illumina StrataMap libraries can be sequenced on the same flow cell if libraries are separated into individual lanes. This page describes how to set up sequencing and analysis when utilizing per-lane loading.

Overview

Autolaunch can initiate analysis for one library per sequencing run. Any additional libraries will need to be launched manually in Core. Alternatively, if autolaunch is not preferred, you may perform a standalone run and manually launch analyses in Core for all individual libraries.

Option 1: Autolaunch one analysis, manually launch additional analyses:

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Option 2: Standalone sequencing run and manually launch all analyses:

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Run Planning for Per-lane Loaded Libraries

Regardless of the chosen approach, the Run Planning tool must be used for each library. Each planned run and sample sheet must contain details for only one library. Attempting to include multiple slides in a single sample sheet will result in an error.

When using the Run Planning tool, follow the instructions on the Run Planning page. For Lane Usage, select only the lanes used by the library instead of all lanes. Unspecified lanes will still be sequenced, but their data will be stored for later access and manual launch in Core.

Example of autolaunch usage in the Run Planning tool for a single library loaded in lanes 3 and 4

Non-standard read lengths

The recommended sequencing configuration for spatial libraries is 130-8-0-0 (100 cycle sequencing kit), however, if a different configuration is needed to share the flowcell with another library, a manual workaround is possible.

The override_cycles and override_reads will need to be adjusted to accommodate the differences. This will depend on the sequencing configuration, but here are some examples:

130:8	I30;N22U7Y71;N8	I30;Y100;I8
200:8	I30;N22U7Y93N48;N8	I30;Y170;I8
300:8	I30;N22U7Y93N148;N8	I30;Y270;I8
150:8:8:150	I30;N22U7Y91;N8;N158	I30;Y120;I8;Y158
250:8:8:250	I30;N22U7Y93N98;N8;N258	I30;Y220;I8;Y258
300:8:8:300	I30;N22U7Y93N148;N8;N308	I30;Y270;I8;Y308

To adjust the override_cycles and override_reads start the analysis manually in Core and update the analysis config file.

Example analysis config file:

{ 
  "override_cycles": "I30;N22U7Y71;N8", 
  "override_reads": "I30;Y100;I8" 
} 

Some example situations:

When sequencing StrataMap libraries, we do not recommend using a read length shorter than 117bp for Read1 for any configuration

Enrichment – Exome (200cycle kit)

Use the 200cycle sequencing kit with a read length structure of 117-10-10-101 (if enrichment library prep utilizes dual 10bp indices) OR 121-8-8-101 (if enrichment library prep utilizes dual 8bp indices). The Statamap and Enrichment – Exome library preps would need to be loaded in separate lanes.

In the analysis_config.json file, the override_cycles and override_reads must be updated to:

117-10-10-101 read length structure:

• "override_cycles": "I30;N22U7Y58;N10;N111"
• "override_reads": "I30;Y87;I10;Y111"

121-8-8-101 read length structure:

• "override_cycles": "I30;N22U7Y62;N8;N109"
• "override_reads": "I30;Y91;I8;Y109"

Whole genome (300cycle kit) The customer would need to use the 300cycle sequencing kit with a read length structure of 151-10-10-151 (if whole genome library prep utilizes dual 10bp indices) OR 151-8-8-151 (if whole genome library prep utilizes dual 8bp indices). The Statamap and Whole genome library preps would need to be loaded in separate lanes.

In the analysis_config.json file, the override_cycles and override_reads must be updated to:

151-10-10-151 read length structure:

• "override_cycles": "I30;N22U7Y58N34;N10;N161"
• "override_reads": "I30;Y121;I10;Y161"

151-8-8-151 read length structure:

• "override_cycles": "I30;N22U7Y58N34;N8;N159"
• "override_reads": "I30;Y121;I8;Y159"