Dragen v3

Manufactured by Illumina

DRAGEN v3.4.12 is a hardware-accelerated bioinformatics platform developed by Illumina. It provides ultra-rapid processing of sequencing data, including alignment, variant calling, and other genomic analysis tasks. The DRAGEN platform is designed to optimize performance and efficiency for a wide range of genomic applications.

Automatically generated - may contain errors

Lab products found in correlation

Novaseq 6000, by Illumina (1 mentions)

Spelling variants of this product

DRAGEN (13 citations) DRAGEN Bio-IT Platform Germline Pipeline v3.0.7 (7 citations) DRAGEN Germline Pipeline v3.2.8 (3 citations) DRAGEN RNA Pipeline v3.7.5 (2 citations) Illumina Dragen v3.10.4a (1 citations)

2 protocols using dragen v3

Variant Extraction from WGS Data

Check if the same lab product or an alternative is used in the 5 most similar protocols

We utilized 98,622 whole genome sequencing (GS) data released on March 15, 2020. The detailed description of GS is available elsewhere⁴⁴. Briefly, the GS data were generated with NovaSeq 6000. DRAGEN v3.4.12 (Illumina) was used for genome alignment and calling, providing 702,668,125 SNVs for 98,622 samples with mean coverage greater or equal to 30x and >90% of bases at 20x coverage. The GS data is available in the All of Us workbench in the Hail matrix. We extracted all variants in PKD1, PKD2, COL4A3, COL4A4, and COL4A5 genes in VCF format using the following hail command in Jupyter Notebook:
We then converted the vcf format data to the bed/bim/fam format using PLINK software^{42 (link)}.

Khan A., Shang N., Nestor J.G., Weng C., Hripcsak G., Harris P.C., Gharavi A.G, & Kiryluk K. (2023). Polygenic risk affects the penetrance of monogenic kidney disease. medRxiv.

+ Open protocol

+ Expand

All of Us Research Program Sequencing

Cited 2 times

Check if the same lab product or an alternative is used in the 5 most similar protocols

Sequencing was performed by the Genome Centers funded by the All of Us Research Program^{14 (link),15 (link)}. All centers used the same sequencing protocols that consisted of PCR-free 150 bp, paired-end libraries sequenced on the Illumina NovaSeq 6000 platform and processed using DRAGEN v3.4.12 (Illumina) software. The GRCh38 reference genome was used for alignment^{16 (link)}. Phenotypic data, ancestry features, and principal components were annotated using Hail through the All of Us Researcher Workbench¹⁷. Low-quality variants with a call rate of less than 0.95, multiallelic variants, and variants significantly departed from Hardy-Weinberg equilibrium in the control cohort (P ≤ 1.0 × 10⁻¹⁰) were removed. Common variants in autosomal chromosomes with a minor allele frequency of higher than 0.005 were included in the association test. Sex concordance was part of the All of Us upstream genomic data quality control process, and all samples within the released genomic data have passed the sex concordance check. Ancestry annotation and relatedness were inferred by the PC-relate method in Hail. Duplicate samples and one of the related participant pairs were excluded¹⁷.

Akçimen F., Chia R., Saez-Atienzar S., Ruffo P., Rasheed M., Ross J.P., Liao C., Ray A., Dion P.A., Scholz S.W., Rouleau G.A, & Traynor B.J. (2023). Genomic analysis identifies risk factors in restless legs syndrome. medRxiv.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!