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.
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.
We are pleased to announce a new release of BaseMount, our FUSE driver to mount your BaseSpace account as a Linux filesystem.
BaseMount allows you to navigate on the command line through projects, samples, runs and app results, and interact directly with the associated files exactly as you would with any other local file system.
BaseMount allows you to download – and now upload – files, but maybe more importantly, it allows you to work interactively with your files stored on BaseSpace without having to download them. You may, for example, run samtools directly on a large BAM file, and it will only fetch the blocks needed for your query.
This update (BaseMount v0.12) includes:
- Write-mode: project and appresult creation, file upload
- Properties can be viewed and edited
- Improved documentation
- Relaxed timeout for low bandwidth
- Unmount assistance, listing blocking processes and offering lazy-unmount
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).