How to set up an AmpliSeq for Illumina run using Local Run Manager v1.3 for MiniSeq

Important note: Version 2 of Local Run Manager is available on-instrument for MiniSeqs instruments that have been updated to MiniSeq Control Software v2 and Windows 10. This bulletin applies only to MiniSeq instruments running version 1 of the control software on Windows 7, which comes pre-installed with Local Run Manager version 1. Local Run Manager version 2 is also available for installation off-instrument and use with MiniSeq data from either version of control software. With the launch of AmpliSeq for Illumina products, we have released DNA Amplicon and RNA Amplicon analysis modules for Local Run Manager version 2. Off-instrument analysis is available for iSeq 100, MiniSeq, MiSeq, and NextSeq 500/550 instruments. Onboard analysis is available for the iSeq 100; MiSeq instruments with MiSeq Control Software version 3 and above; NextSeq 500/500 instruments with NextSeq Control Software version 4; and MiniSeq instruments with MiniSeq Control Software version 2. When sequencing AmpliSeq libraries on a MiniSeq with MiniSeq Control Software version 1 and onboard Local Run Manager version 1.3, data generated on-instrument must be transferred to Local Run Manager 2 off-instrument for local analysis. Demultiplexed FASTQ files can also be uploaded to BaseSpace Sequence Hub for analysis with the DNA Amplicon and RNA Amplicon apps.

To sequence an AmpliSeq for Illumina panel on a MiniSeq with Local Run Manager v1.3, a custom library prep kit must be imported:

1. Download this AmpliSeq.tsv file and save it to the desktop.

2. Log in to the on-instrument Local Run Manager and select Library Prep Kits from the System menu.

3. Select Add Library Prep Kit.

4. Import the AmpliSeq.tsv file.

AmpliSeq for Illumina is now added to your list of available run setup options.

To set up a run:

1. Select Create Run and then GenerateFASTQ.

2. Enter a Run Name.

3. Under Library Prep Kit, select AmpliSeq for Illumina from the dropdown menu.

4. In the table, enter Sample ID and choose the appropriate i5 and i7 indexes from the dropdown menu. Refer to the information from the index plate layout in the Index Adapters Pooling Guide.

5. Optional Adapter Trimming: Local Run Manager version 1.3 for MiniSeq will not automatically perform adapter trimming for imported kits. To trim adapters, select “+ Add custom setting” and add the Adapter option and a sequence for each run using this kit. In the custom settings add Adapter, then in the field next to that add the sequence:

• CTGTCTCTTATACACATCT

1. Select Save Run.

2. In the MiniSeq Control Software, start the run using Local Run Manager mode and select the saved run from the list.

After sequencing, transfer the complete run folder to a computer with off-instrument Local Run Manager 2 with DNA Amplicon and/or RNA Amplicon AmpliSeq modules installed. Refer to the following bulletin for instructions to set up the analysis off-instrument:

• How to set up analysis for AmpliSeq for Illumina libraries with off-instrument Local Run Manager v2

For any feedback or questions regarding this article (Illumina Knowledge Article #2952), contact Illumina Technical Support [e-mail].