Computation backend improvements

We are making some improvements to our computation backend. These changes impact sbg:draft2 tasks only, mostly bringing some of their behaviors/capabilities in line with CWL 1.0 tasks.

Recently published apps

DeepVariant 0.7.2 is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is highly accurate, robust, flexible and easy to use. To use DeepVariant on the CGC, simply supply it with reads, reference, and select the desired model to use (WGS or WES).

Deprecation of Previous Generation instance types

To further optimize user workloads, we have decided to deprecate some of the oldest Previous Generation AWS instances.

Query projects by name in the Python API client

If you are using the sevenbridges-python API client, you are now also able to query projects by project name. When querying with the name parameter, partial matching is performed and the result is returned as a list. See an example in the List Projects section of sevenbridges-python documentation.

Folder options for FTP/HTTP(S) import

When importing data from an FTP or HTTP(S) server to the CGC, you are now able to import an entire folder structure in the exact same form as it appears on its source server, or choose to "flatten" the structure and import the files only. Also, the CGC now provides a selection of naming conflict resolution options for FTP/HTTP(S) imports. If an item that is being imported has the same name as an item already present at the target location, you can select whether to skip importing the item, overwrite the existing one or auto-rename the one that is being imported. Learn more.

R client updates

The sevenbridges-r API client has been updated with several sets of API calls. Precisely, the new additions include Folders, Enterprise, Bulk (partial), Actions and Markers (Advance Access) APIs. Moreover, the R client now also supports setting execution hints per task run when drafting new tasks.

New file search options

When searching for files within a project, now you have the option to search within the current folder only, without including subfolders and their content in the search. Until now, the default behavior was that the current folder (or project root) and all of its subfolders got included in the search, with the Path column being shown in the search results. This remains the default behavior, but now there is an additional option to search through items from the current path (project root or folder) only, without searching through subfolders.

Open apps for editing in web editors more easily

The option to edit apps in the tool or workflow editor on the Platform is now more accessible through the visual interface. When the Edit option is clicked for an app, all sbg:draft-2 apps will be opened in the corresponding web editor by default. However, you still have the option to edit sbg:draft-2 apps in Rabix Composer, our standalone app editor from the Rabix toolkit. For now, Rabix Composer also remains the only editor for CWL 1.0 apps.

Recently published apps

Control-FREEC 11.5

Control-FREEC analyzes copy-number alterations in exome and whole-genome DNA sequencing. This tool computes, normalizes and segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH.

Define compute resources per task run (API)

When creating a task via the API, you are now able to set instance type (top level) and maximum number of parallel instances for your execution without the need to create a new version of the app.

Folders become a standard API feature

Folders are no longer in the Advance Access stage and are available as a standard feature on the API.

Activate spot instances on project creation

When creating a new project through the visual interface, you are now able to set your preference for Spot instance usage in the Create a project dialog. This setting can later be changed from the project settings page, or overridden per task on the draft task page. Learn more about Spot Instances on the CGC.

Data Cruncher - JupyterLab Beta

Data Cruncher is now using the latest release of the JupyterLab environment. All available preinstalled libraries have been updated and some new ones have been added.

We have also made more improvements in order to reduce analysis initialization time. It shouldn't take more than four minutes to spin up your Data Cruncher analysis, regardless of the chosen compute resources.

Updates to the TCGA, TARGET, and CCLE datasets

As part of Seven Bridges' ongoing partnership with the National Cancer Institute (NCI), authorized researchers can access valuable public datasets generated by the TCGA, TARGET, and CCLE initiatives through the CGC, and Seven Bridges collaborates with the NCI Genomic Data Commons (GDC) on an ongoing basis to ensure alignment between the datasets available through the GDC and the CGC. In keeping with this, updated versions of the TCGA, TARGET, and CCLE datasets have been released on the CGC. As of July 10, the legacy TCGA and CCLE datasets available through the CGC are fully aligned with those in the GDC Legacy Archive, and the TCGA GRCh38 and TARGET GRCh38 datasets are fully aligned with GDC Data Release 11.0.

Personal Genome Project UK (PGP-UK) pilot dataset

The Personal Genome Project UK (PGP-UK) pilot dataset includes in-depth multi-omics profiling of thirteen participants, who have been profiled using whole genome sequencing (WGS) of DNA from whole blood, whole genome bisulphite sequencing (WGBS) of DNA methylation from whole blood (WGBS), deep and shallow sequencing of RNA from whole blood using RNA-seq and DNA methylation array profiling of both whole blood and saliva using the HumanMethylation450 BeadChip from Illumina.

The PGP-UK pilot dataset is now available on the CGC under the Public projects tab at the top navigation bar. 

Set null or empty values for app settings

When defining app settings prior to execution, you are now able to set null or empty values for the available inputs. This is possible using the two new buttons placed next to the inputs under the Define App Settings tab.

Variant Browser (BETA)

Variant Browser is under active development with features being added successively. For any suggestions or bug reports, please contact our support team at support@sbgenomics.com.

Variant Browser is an application for genome analysis and interpretation that will allow researchers and clinicians to quickly annotate and accurately prioritize variants and genes involved in a disease. Variant Browser bridges the gap between sequencing/raw data management and clinical management, providing robust genome interpretation to expedite diagnosis and accelerate the understanding of the genetic basis of disease, drug response, and health.

During the BETA stage, you are able to interpret demo VCF files which are readily available inside the app. The available options include filtering with configurable filtering criteria, directly opening the Genome Browser at the position of the selected variant and displaying general statistics for the currently applied filters. In case you want to interpret your own VCF files please contact us at support@sbgenomics.com.

Genome Browser official release

Genome Browser is no longer in the beta stage and has been officially released. The most important achievement in this release is guaranteed accuracy based on manual review of fields in the standard file compared to the most commonly used genome viewer.

Latest additions to Genome Browser also include a history of the last ten positions within the file, easier insertion of markers that takes less clicks than before and the ability to select a different reference file instead of the one that has been preselected based on the headers in the loaded BAM file.

App archiving

We have introduced the option to archive apps that you don't intend to use in a project. Archiving will hide an app from the apps list, workflow editor and other relevant places across the CGC. However, this will not affect reproducibility, as you will be able to rerun existing tasks containing the app.

Multi-Instance Whole Genome Sequencing GATK4.0 Workflow

We’ve published the Multi-Instance Whole Genome Sequencing BWA/GATK 4.0 workflow. This workflow keeps a similar price, with the improvement in total execution time of up to 3.0 times compared to a single-instance implementation. The Multi-Instance Whole Genome Sequencing workflow processes a 30x whole genome in as little time as 3 hours without any additional computational resource such as GPU or FPGA.

Data Cruncher Interactive Analyses - Public project

As a part of the effort to grow a comprehensive set of CGC features and capabilities, we have developed several Data Cruncher Interactive Analyses as an additional resource that should help users mitigate challenges related to interpretation of data obtained through secondary analysis. These Data Cruncher analyses can be found in the Data Cruncher Interactive Analyses public project.

API bulk actions

Due to popular demand, we have created several new API bulk calls. These calls allow users to perform an operation on up to 100 files within a single API call, while using only one API rate limit. This results in significantly faster completion of operations involving a big number of files.

Rabix Composer v1.0 Release

We’ve released the initial version of Rabix Composer (v1.0), which includes significant improvements over the beta version with respect to the development of CWL 1.0 and sbg:draft-2 applications on your local machine.

Set suggested files for workflow inputs

We’ve introduced the option to set files from public projects as suggested for a file input in a workflow. This will allow anyone who runs the workflow to use the suggested files as inputs in a single click, and only have to add the remaining input files manually. Please refer to documentation for more details.

Folders on the visual interface

We have introduced support for folders on the CGC. To complement our existing API functionalities, now you can organize your project files into folders through the CGC's visual interface, which allows you to have a better overview of your files and manage them more easily.

Smart Variant Filtering

The variant filtering process consists of selecting highly confident variants and removing the ones that are falsely called. This process used to be mostly left out from deeper testing in secondary genomic DNA analyses, even though it can boost precision of variant calls significantly. After developing graph genome alignment tool and reassembly variant caller, we are now launching the Smart Variant Filtering tool used for filtering germline variants.