The DRAGEN secondary analysis software utilizes a highly reconfigurable Field Programmable Gate Array (FPGA) card and is available on a preconfigured DRAGEN server that can be seamlessly integrated into bioinformatics workflows. The platform can be loaded with highly optimized algorithms for many different NGS secondary analysis pipelines, including the following:
Whole genome
Exome
RNA-Seq
Methylome
Cancer
All user interaction is accomplished via DRAGEN software that runs on the host server and manages all communication with the FPGA card. This user guide summarizes the technical aspects of the system and provides detailed information for all DRAGEN command line options. If you are working with DRAGEN for the first time, Illumina recommends that you first read the Getting Started section, which provides a short introduction to DRAGEN, including running a test of the server, generating a reference genome, and running example commands.
DRAGEN DNA Pipeline
The DRAGEN DNA Pipeline massively accelerates the secondary analysis of NGS data. For example, the time taken to process an entire human genome at 30x coverage is reduced from approximately 10 hours (using the current industry standard, BWA-MEM+GATK-HC software) to approximately 20 minutes. Time scales linearly with coverage depth.
These pipelines harness the tremendous power of the DRAGEN server and include highly optimized algorithms for mapping, aligning, sorting, duplicate marking, and haplotype variant calling. They also use platform features such as hardware-accelerated compression and optimized BCL conversion, together with the full set of platform tools.
Unlike all other secondary analysis methods, DRAGEN DNA Applications do not reduce accuracy to achieve speed improvements. Accuracy for both SNPs and INDELs is improved over that of BWA-MEM+GATK-HC in side-by-side comparisons.
In addition to haplotype variant calling, the pipeline supports calling of copy number and structural variants as well as detection of repeat expansions.
DRAGEN secondary anaylsis includes an RNA-seq (splicing-aware) aligner, as well as RNA-specific analysis components for gene expression quantification and gene fusion detection.
The DRAGEN RNA Pipeline shares many components with the DNA Pipeline. Mapping of short seed sequences from RNA-Seq reads is performed similarly to mapping DNA reads. In addition, splice junctions (the joining of noncontiguous exons in RNA transcripts) near the mapped seeds are detected and incorporated into the full read alignments.
DRAGEN secondary analysis uses hardware accelerated algorithms to map and align RNA-Seq--based reads faster and more accurately than popular software tools. For instance, it can align 100 million paired-end RNA-Seq--based reads in about three minutes. With simulated benchmark RNA-Seq data sets, its splice junction sensitivity and specificity are unsurpassed.
The DRAGEN Methylation Pipeline provides support for automating the processing of bisulfite sequencing data to generate a BAM with the tags required for methylation analysis and reports detailing the locations with methylated cytosines.
