Release notes

NewSpatial Transcriptomics Pipeline with Spotty

Spatial Transcriptomics is a method that allows visualization and quantitative analysis of the transcriptome in individual tissue sections. Spatial Transcriptomics Pipeline with Spotty is a workflow for processing raw sequence data (paired FASTQ-files) generated using the Spatial Transcriptomics technology. The workflow produces a table of spatially distributed gene counts for downstream analysis.

This workflow consists of two nested workflows:

1. ST Pipeline which performs demultiplexing and decoding of the RNA-Seq reads.
2. The Spotty workflow with post processing, to perform automatic spot identification and pairing between the fluorescent (Cy3) and tissue (HE) image. Spotty is proprietary and available only on the Seven Bridges platform environments.

Read more about the workflow on our blog.

NewData Cruncher Interactive Analyses – Public project

As a part of the effort to grow a comprehensive set of platform 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.

The project contains five analyses:

• Ballgown Interactive Analysis
• VCF visualization Interactive Analysis
• Structural variation Interactive Analysis
• ChIP-seq Interactive Analysis
• Microbiome Differential Abundance Analysis

Each Interactive Analysis comes with explanations of analysis steps and a corresponding set of files needed for successful execution.

NewSupported instances update

The new generation of AWS EC2 Compute Optimized instances (C5) and General Purpose instances (M5) is now also available in task executions and Data Cruncher analyses on eu.sbgenomics.com. See the full list of supported AWS EU instances in our documentation.

NewAPI bulk actions

Due to popular demand, we have created several new API bulk calls. The 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.

Currently we have bulk calls implemented for the following operations:

• bulk imports from a volume
• bulk exports to a volume
• bulk get file details (stat files)
• bulk delete files
• bulk edit files

The calls have also been implemented in our Python client, with Java and R client implementation coming up in the near future.

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.

For more details about the Rabix Composer v1.0 release, please refer to the latest Rabix release note. Also, keep an eye out for further updates and improvements to this initial release.

Key new features in Rabix Composer v1.0:

• We have integrated Rabix Executor into the Composer, so you can now develop and test your CWL app through a single user interface.
• When you edit a tool or workflow on the Seven Bridges Platform, you will see the Edit with Rabix Composer button.
• Rabix Composer is now also available for Windows.

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 Seven Bridges Platform. To complement our existing API functionalities, now you can organize your project files into folders through the Platform’s visual interface, which allows you to have a better overview of your files and manage them more easily. Some of the currently available options related to folders are the ability to copy and move files between folders, use the optional sidebar tree for browsing, search recursively inside the folder structure and use files from folders as task inputs. In the upcoming period we will be working on adding more options to folders, such as the ability to rename a folder, output task results into a folder and many more.

Uploaders have also undergone some changes in order to add folder support. Two major features are introduced:

• uploading items (files and/or folders) into folders;
• preserving folder structure when uploading items.

Both of these features are introduced in CLI and Desktop Uploaders.

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.

Smart Variant Filtering (SVF) uses machine learning algorithms trained on features from the existing Genome In A Bottle (GIAB) variant-called samples (HG001-HG005) to perform variant filtering (classification). The comparison results obtained during deep, three-stage testing demonstrate that it outperforms the solutions currently used within most secondary DNA analyses. Smart Variant Filtering increases the precision of called SNVs (removes false positives) by up to 0.2% points while keeping the overall f-score higher by 0.12-0.27% points than in existing solutions.

Learn more about the Smart Variant Filtering public project from our documentation.

TLS 1.0 and TLS 1.1 no longer supported

We have removed support for TLS 1.0 and TLS 1.1 protocols. The only supported protocol on our Platform and API is TLS 1.2. If you are using a client that does not support TLS 1.2, please perform an upgrade to continue using the Seven Bridges Platform.

More about the TLS protocol

The TLS (Transport Layer Security) protocol is a cryptographic protocol that provides communications security in a computer network. It’s a successor of the SSL (Secure Sockets Layer) protocol that is now prohibited from use by IETF. TLS provides both confidentiality and data integrity in transit between two communicating computers. TLS version 1.2 is a modern version of this protocol that enables highest possible communication security between your application/browser and our Platform/API. The deprecated versions, TLS 1.0 and TLS 1.1, have a number of known weaknesses, and it is in the best interest of our users to use the up-to-date version.

Supported clients

If you are using Internet Explorer, make sure that you upgrade your browser to version 11 or later. If you are using an up-to-date version of Chrome, Firefox or Safari – you are all set.

If you have any follow-up questions, feel free to contact the Seven Bridges Support Team.

ImprovementsFile page improvements

Now, you can view html, b64html, RNA vis index, ingenuity report, bench SQLite, PDF, GIF, JPEG, SVG, PNG, and ipynb files from the File page without downloading the file. Please be aware when opening files for preview or when downloading files that they are from a trusted source.

Note that file metadata is now collapsed by default. Click on the info icon in the top right to view file metadata.
Please contact support@sbgenomics.com for any file-related issues.

NewQuery with search terms

We’ve improved querying datasets via the Data Browser. After selecting one or more datasets, you can use search terms to start your query. Terms will autocomplete as you type and suggest Keywords, Related queries, and Saved and example queries. Select a query from Related queries or Saved and examples. Or, enter more keywords and hit enter to choose a pre-built query from the Results page. This intuitive feature enables users to familiarize themselves with the Data Browser and lowers the learning curve to query building.

Learn more from our documentation.

NewSupported instances update

We now support the use of new generation AWS EC2 Compute Optimized instances (C5) and General Purpose instances (M5) in task executions and Data Cruncher analyses on the Seven Bridges Platform. Note that these instances are not available on eu.sbgenomics.com.