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Edico Genome’s DRAGEN Bio-IT Platform Now Available on BaseSpace® Sequence Hub

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.

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Figure 1

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.

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Advancing cancer research with new BaseSpace® Sequence Hub Apps 

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.

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VCAT v3.0 and FASTQ Toolkit v2.2 – Usability Improvements and Gold Reference Updates

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

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Introducing Enrichment v3.0 with Enhanced Variant Calling

Enrichment

Enrichment v3.0

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

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New RNA-Seq Alignment App with support for TruSight RNA Pan-Cancer and more

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.

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RNA-Seq Alignment

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Human mtDNA Analysis in BaseSpace

Mitochondrial DNA (mtDNA) analysis enables forensic laboratories to extract genetic data from small biological samples, found in less than ideal condition. Mitochondria in humans cell contain about 1,000 copies of mtDNA. The ease-of-use of next-generation sequencing (NGS) and Nextera XT enables labs to speed up their workflow, reducing time and labor spent on prep, and generate deeper coverage data compared to Sanger sequencing at 1X coverage/rx.

The updated Illumina mtDNA demonstrated protocols provide a complete mitochondrial DNA solution – from targeted library prep and sequencing to bioinformatics analysis and report generation in BaseSpace – to help investigators draw conclusions in a straightforward and intuitive workflow.

The two new mtDNA apps in BaseSpace allow for variant analysis and easy visualization of mitochondrial sequence data. This workflow can analyze any part of the full circular genome, without any origin dead zone, using quality and coverage thresholds customized by the user (Figure 1).

Figure 1: mtDNA Analysis Workflow. Sequence data is streamed into BaseSpace. Initial processing is performed using the mtDNA Variant Processor app and the results are stored in your BaseSpace project. Use mtDNA Variant Analyzer to visualize the data and generate a downloadable Excel report.

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