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
Early next week all BaseSpace Sequence Hub accounts will track storage and compute usage.
Our Basic tier users will continue to enjoy 1 Terabyte of storage for free. On top of that we’re crediting your account with 250 free iCredits to use over 30 days to make sure you have a chance to explore all the apps we offer*.
We offer several compute and storage options to fit your needs. Let us know if you’d like to learn more about BaseSpace Sequence Hub tiers.
* iCredits are used to pay for app compute charges. Any unused iCredits will expire at the end of this 30 day period.
We are pleased to announce the third release (version 0.8) of BaseSpaceCLI, which includes a major new tool and a number of minor features. To install the new release, run this script:
$ sudo bash -c "$(curl -L https://bintray.com/artifact/download/basespace/helper/install.sh)"
With this release of BaseSpaceCLI we are introducing a new high-performance copy tool called BaseSpace Copy or bscp, which provides the following features:
- Rich and flexible URI mechanism to specify source and target for copies
- Multi-threaded for performance and to cope with high-latency connections
- Excellent data integrity, all part data is hashed and verified. Ability to export md5sum compatible sum file for future data verification.
- Resumable downloading
Accelerates discovery by demonstrating genetic functional relationships and validating results
Illumina and Elsevier R&D Solutions have announced a collaboration to integrate use of Pathway Studio, Elsevier’s database of experimental data and disease models, with Illumina’s BaseSpace Correlation Engine platform, offering them as one seamless solution. Under the terms of the agreement, all licensed Correlation Engine users have free access to Pathway Viewer, an application that enables researchers to quickly view a snapshot of the functional relationships among genes. In addition, researchers are able to find top scoring canonical pathways that correlate most highly with the genes list.
Correlation Engine is a suite of applications that lets users discover the relationships among their results, with billions of correlations derived from the world’s largest curated library of genomic knowledge. The applications contain over 130,000 experimental comparisons from more than a half million samples, drawn from NCBI’s Gene Expression Omnibus and other open-access or controlled-access databases.
We’ve recently added some improvements to the Sequencing Runs list. These updates should help to quickly get basic quality information about each run, without needing to click into Run details pages.
For example, % reads passed filter (%PF), average %Q30, yield, and cycles (for Read1 and Read2) are now columns on the Runs list.