Join us for our upcoming webinar: High-volume sequence analysis with BaseSpace™ Sequence Hub and Edico DRAGEN apps, on Dec 13 at 10AM (PT)
The latest sequencing technologies enable unprecedented throughput and redefine limits for many labs. To adapt, these labs must redefine how they work – by automating tasks to reduce touchpoints and by simplifying workflows with integration and robust analysis tools.
In this webinar, we describe BaseSpace™Sequence Hub and how the newest features support high throughput, high-volume sequencing. We demonstrate how customers can progress from flowcell loading to variant analysis with zero touchpoints by using the Whole Genome Sequencing or Edico DRAGEN apps. Additionally, we describe how the integration with BaseSpace™ Variant Interpreter enables users to interpret and generate reports of identified variants.
For Research Use Only. Not for use in diagnostic procedures.
Bioinfomatics tools are a key component in the Next-generation Sequencing (NGS) workflow and can have a significant impact on the results. Alignment and variant calling, in particular, involve complex algorithms, each with unique strengths and weaknesses. The Broad Institute’s BWA+GATK application is among the most popular, but over the last few years more alignment+variant calling methods have been released by companies including Illumina, Edico Genome, and Sentieon. With the emergence of multiple methods comes a clear need for comparison between the results obtained by these methods so that people who use these tools can select the best one for their purpose.
The new Hap.py app available on BaseSpace Sequence Hub enables users to compare diploid genotypes at the haplotype level by generating and matching alternate sequences in a small region of the genome that contains one or more variants. Hap.py makes it easy to compare any variant call set against a range of packaged gold-standard truth sets1,2 to perform routine benchmarking.
Removing the NGS Analytics Data Bottleneck with Field-Programmable Gate Arrays (FPGAs)
The following is a guest blog, written by our partners at Edico Genome.
The next-generation sequencing (NGS) analysis demand is growing at an exponential rate, creating a shortage of computing power to analyze the rapidly growing body of data. Current projections1 calculate genomic data to continue doubling every seven months, a stark acceleration in comparison to Moore’s Law, which states CPU capabilities will double every two years (Figure 1, below). The void left in-between creates a bottleneck for genomics labs.
Providing an alternative to traditional CPU-based systems, Edico Genome’s DRAGEN™ (Dynamic Read Analysis for Genomics) Platform leverages FPGA (Field-Programmable Gate Array) technology to provide customers with hardware-accelerated implementation of genome pipeline algorithms. Leveraging FPGAs, DRAGEN allows customers to analyze NGS data at unprecedented speeds with extremely high accuracy2 onsite, in the cloud, or through a blended hybrid cloud.
BaseSpace Sequence Hub, hosted on Amazon Web Services, enables the cloud-based deployment of the Edico Genome DRAGEN pipeline. Edico Genome’s DRAGEN Genome Pipeline is now readily available, enabling rapid analysis of whole genome sequencing and targeted resequencing panels.
Analyzing the genetic basis of a given tumor is important for understanding the progression of cancer and developing new methods of treatment. Cancer researchers use a variety of methods but none of them efficiently cover all of the variations present in our genes. To help researchers address this challenge, Illumina offers TruSight® Tumor 170, a next-generation sequencing (NGS) assay designed to cover 170 genes associated with cancer.
To help TruSight Tumor customers analyze data from this assay, we are excited to announce two new apps in BaseSpace Sequence Hub:
Additionally, we have made a significant update to the Tumor Normal app. All 3 apps expand our portfolio of cancer research applications by delivering advanced, new methods NGS data generation and analysis.
The Variant Calling Assessment Tool (VCAT) v3.0 BaseSpace® App has improved usability, several new gold references, adds BED file stratification, and delivers an enhanced in-browser report.
Improved VCF file selection
- File chooser now allows multi-selection of VCFs
- Easier usage of alternative labels for VCF files
- File chooser now defaults to the current Project
- Improved VCF file tooltips now show analysis name
Gold Reference Additions and Updates
- Added Platinum Genomes reference data for NA12877 (male spouse of NA12878)
- Added NIST GiaB gold reference data for NA24385 (Ashkenazi male)
- Added gold reference data and novelty rate calculations for hg38
- Updated NIST Genome in a Bottle reference data to version 3.2.2
- Updated Platinum Genomes reference data to version 2016-01
The new Enrichment v3.0 BaseSpace® App (formerly called Isaac Enrichment) introduces major improvements and new features including:
- Improved small variant calling
- Copy number variant (CNV) calling
- Structural variant calling
- Somatic/low-frequency variant calling
- Ability to start from FASTQ or BAM
- GRCh38 reference added
- Variant table CSV file including variant frequencies
- Improved variant annotation engine
- Improved metrics engine
With the launch of the TruSight RNA Pan-Cancer panel, a targeted enrichment panel for the detection of variants, fusions, and gene expression profiles in 1385 cancer-associated genes, Illumina is pleased to provide an intuitive BaseSpace App, RNA-Seq Alignment v 1.0, that supports simple push button analysis of the data.