Different options/apps/pipelines available on the MiSeq i100, Nextseq2000, NovaSeqX, DRAGEN on BaseSpace, DRAGEN server and on Illumina Connected Analytics (ICA)
The table below describes the different options of the DRAGEN pipeline which can be used on Basespace vs DRAGEN on-board instruments. In addition, the table also includes the options for DRAGEN on DRAGEN server and ICA (Illumina Connected Analytics):
The Wave 2 (2026) MiSeq i100 Series will offer sample-to-analysis workflows that include library prep kits, panels, sequencing on the MiSeq i100 Series, and DRAGEN secondary analysis. Data analysis summaries are generated in two hours or less for most applications.
Onboard DRAGEN applications include:
• DRAGEN BCL Convert
• DRAGEN Library QC
• DRAGEN small WGS
• DRAGEN Microbial Enrichment Plus
• DRAGEN 16S Plus
• DRAGEN Microbial Amplicon
• DRAGEN Metagenomics Pipeline
• DRAGEN Amplicon
• DRAGEN Enrichment
The table below describes general information about DRAGEN pipeline/Variant Type detected and metrics provided:
| Pipeline | Description | Variant Types Detected | Metrics Provided | | DRAGEN Demultiplexing | Rapid demultiplexing of NGS analysis | N/A | N/A | | DRAGEN Compression | DRAGEN ORA compression is optimized for high compression ratios of FASTQ files, as well as rapid compression and decompression, all while preserving data integrity. | N/A | Compression RatioRun Time | | DRAGEN Map + Align | The DRAGEN Map + Align can be run as a standalone or as part of DRAGEN’s suite of pipelines | N/A | Mapping metricsDuration MetricsCoverage Metrics | | DRAGEN Germline | The DRAGEN Germline Pipeline provides end-to-end NGS analysis, including advanced error model calibration for increased accuracy, and repeat expansion detection and genotyping through Illumina Expansion Hunter. | SNVIndelCNVSVRepeat Expansions | Mapping metricsDuration MetricsCoverage MetricsVariant MetricsCallability Report | | DRAGEN Somatic | The DRAGEN Somatic Pipeline includes tumor-only and tumor-normal modes, designed for detecting somatic variants in tumor samples. Both modes make no ploidy assumptions, enabling detection of low-frequency alleles. | SNVIndelCNVSVTMBMSIHLA | Mapping metricsDuration MetricsCoverage MetricsVariant MetricsCallability Report | | DRAGEN Enrichment | The DRAGEN Enrichment Pipeline combines DRAGEN’s germline and somatic callers into a pipeline designed specifically for analyzing enrichment samples. Includes a full suite of enrichment metrics and reporting. | SNVIndelCNVSV | Mapping metricsDuration MetricsCoverage MetricsVariant MetricsCallability Report | | DRAGEN RNA | The DRAGEN RNA Pipeline performs transcriptome analysis starting with splice junction discovery and alignment, followed by rapid alignment and splice junction mapping and quantification. For differential expression, Illumina recommends the DRAGEN Differential Expression app on BaseSpace Sequence Hub. | SNVIndelGene fusion | Mapping metricsDuration MetricsCoverage MetricsVariant MetricsCallability Report | | DRAGEN Single Cell RNA | The DRAGEN Single Cell RNA pipeline performs demultiplexing, cell-barcode and UMI error correction, sequence alignment, and quantification of gene expression. | N/A | Mapping MetricsDuration MetricsCoverage MetricsCallability ReportCell Metrics | | DRAGEN Joint Genotyping | The DRAGEN Joint Genotyping/Population Pipeline calls variants jointly across multiple genomes and scales to large cohorts of samples at expedited speeds with uncompromising accuracy. | SNVCNVSVRepeat Expansions | Mapping metricsDuration MetricsCoverage MetricsVariant MetricsCallability Report | | DRAGEN Methylation | The DRAGEN Methylation Pipeline performs alignment, methyl calling, and calculates alignment and methylation metrics. | N/A | Mapping metricsDuration MetricsCoverage MetricsVariant MetricsCallability Report | | DRAGEN Reference Builder | Accepts FASTA files, and builds the proprietary reference used by the DRAGEN apps. | N/A | N/A | | DRAGEN TruSight Oncology 500 ctDNA Analysis Software | Secondary analysis support for Illumina’s TruSight Oncology 500 ctDNA. Only available on the local DRAGEN Server (version 3) | SNVIndelCNVDNA fusionsMSITMB | Mapping metricsDuration MetricsCoverage MetricsVariant MetricsCallability Report | | DRAGEN Imputation | The DRAGEN Imputation pipeline is an end to end user friendly tool that enables scalable low pass whole genome sequencing analysis | SNVIndel | Impute ≤100 samples simultaneously 1.7x faster compared to original GLIMPSE code |
For any feedback or questions regarding this article (Illumina Knowledge Article #5165), contact Illumina Technical Support [email protected].
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