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.
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).