BaseMount: A Linux command line interface for BaseSpace

BaseSpace was designed with a graphical, web-based interface to enable push-button analytics, and sharing of NGS data. We also realize that there are some use cases, especially while working with bulk data, where a Linux-based command line interface (CLI) is more convenient.  We are therefore happy to announce the early access release of BaseMount, a tool that can be used to mount your BaseSpace data as a Linux file system. With BaseMount you can navigate 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 is a FUSE driver, which operates in user-space and uses the BaseSpace API to generate the file system structure for both the metadata and actual file-based data.

To install, please go to the BaseMount page: basemount.basespace.illumina.com and run the installation script. We have several tutorial videos as well as a Help Page to get you started. The Help page also has information on hardware and operation system requirements.

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Illumina software now available under GPL v3

We are excited to announce that we will be contributing Illumina’s secondary analysis software to the open source community under the GPL v3 license. The software can be found on GitHub (https://github.com/illumina). Currently available software include the Isaac aligner and the Manta structural variant caller (manuscript submitted). Other tools such as the Starling small variant caller, Strelka somatic variant caller, the Canvas copy number caller, and Haplotype Compare (a.k.a hap.py) for comparing variant call sets will be made available soon. Additional tools will also be made available as they are developed and deployed. With these efforts we are also committing to publication of our methods in high impact peer reviewed journals.

We look forward to working with the open source community to provide high quality secondary analysis tools that will help enable discoveries with next generation sequencing data.

 

Introducing App Versioning

We’re excited to announce support for versions of BaseSpace apps. The App Store has been very successful, and with this success comes the need to publish improved versions of apps.

Every app will now have a single entry in the App Store, and you may choose the version on each App Description page.

app-launch-menu

Each app version will have two new sections on the App Description page. The “Release Notes” section will list the changes since the last version. And the optional “What’s New” section can contain the latest updates about a version, such as bugs discovered since publication or changes to the version’s price.

isaac-enrichment

It’s important that once app versions are published, they can no longer be changed. This way apps can be used to analyze many samples in exactly the same way.

We’ve added some features to ensure that samples can be analyzed consistently during experiments. If you navigate to the App Description page of an app you’ve launched before, your default view will be the version that you launched the last time. Also, once an app version is published, it can no longer be changed by developers. Bug fixes and improvements can be added in new versions.

We’ll let you know if a new version is available. If you are on the App Description page of an older version, you will be notified that a new version is available.

app-launch-notification

App developers will notice some nice improvements to our developer portal, which include a new page to create and view app versions.

devportal

We hope you find these changes useful, and we all look forward to improved versions of apps!

Overhaul of SAV Charts

As part of the latest release of BaseSpace, we have made some changes to the Run charts by adding interactive functionalities such as zoom, pan, and scale for certain charts.

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MethylSeq v1.0 App for DNA Methylation Calling

DNA methylation is one of the most studied epigenetic modifications in human cells. Changes in DNA methylation patterns play a critical role in development, differentiation and diseases such as multiple sclerosis, diabetes, schizophrenia, aging, and multiple forms of cancer. Over the past decade, interest in DNA methylation has grown rapidly and expanded across multiple areas of research. Consequently, DNA methylation analysis methods have undergone dramatic changes. Bisulfite-treatment and next-generation sequencing (NGS) have increasingly become the tools of choice to profile DNA methylation levels. Here, we announce a bioinformatics solution for analyzing NGS methylation data: BaseSpace® MethylSeq v1.0 app.

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MethylSeq v1.0 app

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Submit Data from BaseSpace to NCBI’s Sequence Read Archive

When sequencing data supports a new finding that is reported to the scientific community, it is common practice to share the sequencing data that generated the result, through an archive such as NCBI’s Sequence Read Archive. How would a BaseSpace user do this? Until now, a BaseSpace user would have to download their data locally, and then prepare an SRA submission through NCBI’s published guidelines.

SRA Submission App

Since BaseSpace already stores some of the metadata that go into a submission, we felt we could make this process easier. Today, we’re excited to announce the release of the SRA Submission App, a BaseSpace Labs release. Built in collaboration with NCBI, the app prepares your submission XML and transfers the data directly to SRA from BaseSpace. Read More…

New RNA Apps in BaseSpace

We are excited to launch the TruSeq Targeted RNA v1.0 and Small RNA v1.0 Core Apps in BaseSpace, which are some of the most feature-rich Apps we have launched to date.

 

TruSeq Targeted RNA v1.0

Small RNA v1.0

A high level overview of the Apps is provided below. More detailed information about the Apps can be found in their respective Core Apps application guides.

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