Illumina Preset Protocols v2.8 Installation and User Configuration

The Illumina Preset Protocols (IPP) v2.8 support the integration of Clarity LIMS with established lab protocols.

The integration provides preconfigured workflows that map to lab protocols and steps, and support Illumina library prep kits, reagent kits, assays, and instruments.

This guide provides instructions and describes the components installed in the default configuration of IPP.

IPP Integration v2.8 is distributed as the BaseSpaceLIMS-Illumina-Preset-Protocols RPM package. The RPM package installs the following components:

• The illumina-preset-protocols-installer.sh script for configuration slices.
• Templates for the following uses:
– Sample sheet generation
– Sample placement pattern
– Covid testing setup and reporting
– Illumina Genomics Architecture (IGA)
• Automation scripts, including scripts to support IGA and Clarity LIMS Product Analytics (CLPA) automation.
• Configuration slices.
• Workflows for applicable instrument integrations.
• BCL2FASTQ_Reverse_Complement_Samplesheet.csv
• BCL2FASTQ_Samplesheet.csv
• genomeStudio_Genotyping_SampleSheet_driver_file.csv
• genomeStudio_Methylation_SampleSheet_driver_file.csv
• iSeq_Samplesheet.csv
• iSeqManual_Samplesheet.csv
• miniSeq_Samplesheet.csv
• MiSeqSamplesheetv3.csv
• NextSeq1K2K_Pool1.csv
• NextSeq1K2K_Pool2.csv
• NextSeq1K2K_Pool3.csv
• NovaSeq_BCL2FASTQ_Samplesheet.csv
• NovaSeq_BCL2FASTQ_Samplesheet_v2.csv
• NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv
• NovaSeq_Standard_Bulk_Pool1.csv
• NovaSeq_Standard_Bulk_Pool2.csv
• NovaSeq_Standard_Bulk_Pool3.csv
• NovaSeq_Xp_Bulk_Pool.csv
• NovaSeq_Xp_Bulk_Pool2.csv
• NovaSeq_Xp_Working_Pool.csv
• NovaSeq_Xp_Working_Pool2.csv
• NovaSeqDx_BCL2FASTQ_Samplesheet_v2.csv
• NovaSeqXSeries_Bulk_Pool1.csv
• NovaSeqXSeries_Bulk_Pool2.csv
• NovaSeqXSeries_Dilute_Denature_Calculate_Volumes.csv
• NextSeq1K2K_OnPrem_Samplesheet.csv
• Hybrid Pattern_96 well plate_8x1 HD BeadChip.tsv
• Hybrid Pattern_96 well plate_8x1 LCG BeadChip.tsv
• Hybrid Pattern_96 well plate_12x1 HD BeadChip.tsv
• Hybrid Pattern_96 well plate_24x1 HD BeadChip.tsv
• Hybrid Pattern_96 well plate_24x1 HTS BeadChip.tsv
• Hybrid Pattern_96 well plate_24x1 HTS BeadChip Multichannel.tsv
• Hybrid Pattern_96 well plate_24x4 XT BeadChip.tsv
• 7900sds_container_setup_template.txt
• covid_report_results.csv
• BatchingInputFile_template.csv
• CaptureWashInputFile_template.csv
• ExtractionInputFile_template.csv
• LibInputFile_NFE_template_withoffsets.csv
• LibInputFile_NFPF_template_withoffsets.csv
• LoadToFlowcell_NovaSeqXp_Incomplete_template.csv
• LoadToFlowcell_NovaSeqXp_ManifestForConsolidation_template.csv
• LoadToFlowcell_NovaSeqXp_template.csv
• LoadToLibTubeFile_NovaSeqStd_template.csv
• MakeBPFile_NovaSeq_template.csv
• PlatingInputFile_template.csv
• autoPlaceCovid7500.py
• clarityapiutil.py
• parseCovidSeqRunReport.py
• verifyBeadChipIDs.py
• glsapiutil, which includes the following scripts:
– glsapiutil.py
– glsapiutil3.py
• hamilton_fast_prep, which includes the following scripts:
– 01_A_CFP_Batching_defaultContainerCheck.py
– 01_CFP_Batching_confirmPlateID.py
– 01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py
– 02_ReagentParsing.py
– 03_checkHamiltonFileNameBarcode.py
– 04_A_checkIndexPlateBarcodeWithCategory.py
– 04_B_autoAssignIndexesFromIndexPlanning.py
– 05_reusedIndexPlateWarning.py
– countSamples.py
– countSamplesInPools.py
– validate_sample_placement.py
• iga_helpers, which includes the following scripts:
– clarityUIFileHelper.py
– pop_up_msg.py
– printCurrentWorkflow.py
• iga_novaseq, which includes the following scripts:
– 01_NovaSeqStd_confirmPlateIDAndStoreInstrumentID_OptionalFile.py
– 02_NovaSeqStd_confirmPlateIDAndStoreInstrumentID_OptionalFile_DiluteDenature.py
– 03_NovaSeqXp_confirmBPPPlateAndStoreInstrumentID.py
– 03_NovaSeqXp_consolidateBulkPoolFiles.py
– 04_NovaSeqXp_completeAndConsolidateWPPZipFile.py
– NovaSeq_automated_warning.py
– NovaSeq_pooling_warning.py
– validate_floorcell_container.py
– validate_flowcell_pools.py
– validate_multiple_destination_plates.py
• illumina-cobalt-samplesheet-converter, which includes the following scripts:
– ss_converter
– converter.py
– errors.py
– v1_builder_plugins.py
– v1_v2_handler.py
– v2_converter_plugins.py
• index_correct, which includes the apply_correction_factors.py script.
• make_bpp, which includes the following scripts:
– apply_multiple_bulk_pools.py
– calculate_sample_volume.py
• utils, which includes the following scripts:
– common.py
– igaapiutil.py
• unified-product-analytics-automation.jar

The following configuration slices are included in IPP Integration v2.8:

• Illumina_Instruments, including:
– iScan-v1.0
– iSeq-100-v1.0
– Library-Prep-Validation-v2.3
– miniSeq-v1.0
– miseq-v3.2
– NextSeq1k2k-v2.4
– nextseq550-v1.1
– novaseq-v3.8
– novaseqdx-v1.2
– NovaSeqXSeries-v1.1
– NextSeq1k2kOnPrem-v1.0
• QC_Protocols
– qc-protocols
• Ampliseq_for_Illumina_Protocols, including:
– AmpliSeq-Illumina-BRCA-Panel-v1.1
– AmpliSeq-Illumina-Cancer-HotSpot-Panel-V2-v1.1
– AmpliSeq-Illumina-Childhood-Cancer-Panel-v1.1
– AmpliSeq-Illumina-Comprehensive-Cancer-Panel-v1.1
– AmpliSeq-Illumina-Comprehensive-Panel-v3-v1.1
– AmpliSeq-Illumina-Custom-DNA-Panel-v1.1
– AmpliSeq-Illumina-Focus-Panel-v1.1
– AmpliSeq-Illumina-Immune-Repertoire-Panel-v1.1
– AmpliSeq-Illumina-Immune-Response-Panel-v1.1
– AmpliSeq-Illumina-Myeloid-Panel-v1.1
– AmpliSeq-Illumina-TCR-beta-SR-Panel-v1.1
– AmpliSeq-Illumina-Transcriptome-Human-Gene-Expression-Panel-v1.1
• Covid, including:
– CDC-COVID-19-RT-PCR-v1.1
– Illumina-COVIDSeq-Workflow-v1.6
– Respiratory-Virus-Panel-v1.0
• DNA_Protocols, including:
– ILASS-TruSight-Whole-Genome-Assay-v1.2
– Illumina-DNA-PCR-Free-Library-Prep-Manual-v1.0
– Illumina-DNA-Prep-M-Tagmentation-v1.0
– Nextera-Mate-Pair-v1.0
– Nextera-XT-v2.0
– TruSeq-DNA-PCR-Free-v2.0
– TruSeq-Nano-DNA-v1.0
• IGA, including:
– IGA_Library_Prep_Automated_v2.1
– IGA_NovaSeq_Sequencing_v2.2
• Infinium_Array, including:
– Genome-Studio-v1.0
– ILASS-Infinium-Genotyping-Assay-v1.0
– Infinium-HD-Methylation-Assay-Manual-v1.2
– Infinium-HTS-Assay-Manual-v1.2
– Infinium-LCG-Assay-Manual-v1.2
– Infinium-XT-Assay-Manual-v1.2
• Methylation_Protocols, including:
– TruSeq-ChIP-Seq-v1.0
– TruSeq-Methyl-Capture-EPIC-v2.0
• RNA_Protocols, including:
– Illumina-Stranded-mRNA-Prep-Ligation-v1.1
– Illumina-Stranded-Total-RNA-Prep-Ligation-with-Ribo-Zero-Plus-v1.1
– TruSeq-Small-RNA-v1.0
– TruSeq-Stranded-mRNA-v2.1
• Targeted_Amplicon_Protocols
– TruSeq-Custom-Amplicon-v1.0
• Targeted_Enrichment_Protocols, including:
– Illumina-DNA-Prep-with-Enrichment-S-Tagmentation-v1.2
– Illumina-RNA-Prep-with-Enrichment-L-Tagmentation-v1.1
– Nextera-Rapid-Capture-Custom-Enrichment-v2.0
– TruSeq-DNA-Exome-v2.0
– TruSeq-RNA-Exome-v1.0
• TruSight_Oncology_Protocols, including:
– TruSight-Oncology-500-ctDNA-v1.1
– TruSight-Oncology-500-HT-v1.1
– TruSight-Oncology-500-v1.1
– TruSight-Tumor-170-v2.0

IPP Integration v2.8 contains workflows that are used to integrate the following instruments:

• iScan
• iSeq
• MiSeq
• MiniSeq
• NextSeq 500/550
• NextSeq 1000/2000
• NovaSeq 6000
• NovaSeq 6000Dx
• NovaSeq X Series

The following workflows are included in the integration:

• iScan v1.0
• iSeq 100 v1.0
• Library Prep Validation v2.3.3
• MiniSeq v1.0
• MiSeq Sequencing v3.2
• NextSeq 500/550 Sequencing v1.1
• NovaSeq 6000 v3.8
• NextSeq 1000/2000 Sequencing v2.4
• NovaSeqDx v1.2
• NovaSeq X Series Sequencing v1.1
• NextSeq 1000/2000 On-Prem Sequencing v1.0

These workflows require ClarityLIMS-NGS-Package v5.25 or later so that the Template File Generator tool can be used.

For more information on each instrument, refer to the Clarity LIMS Integrations and Tool Kits documentation.