Release notes

ImprovementsRHEO – improved scaling and more elastic execution infrastructure

We have improved our automation execution infrastructure by enabling it to scale up its compute capacity automatically when there is an increased workload and a need for new automation runs to be initialized. In addition, we have introduced a limit of 30 parallel automation runs per Division as a measure of precaution to ensure proper use of the elastic automation execution service. Executions that require more than 30 parallel runs are still absolutely possible, as the limit can be increased if there is an actual need for more capacity. Please contact support@sevenbridges.com for more details.

AWS i3 instances available on all environments

With this update you can use the newest Amazon EC2 I3 instances designed for data-intensive, high transaction, low latency workloads, offering the best price per I/O performance (I3) and the lowest price per GB of SSD instance storage on Amazon EC2 (I3en).

The following instances have been added:

• i3.large
• i3.xlarge
• i3.2xlarge
• i3.4xlarge
• i3.8xlarge
• i3.16xlarge
• i3en.large
• i3en.xlarge
• i3en.2xlarge
• i3en.3xlarge
• i3en.6xlarge
• i3en.12xlarge
• i3en.24xlarge

Learn more about supported AWS instance types.

Recently published apps

We have published GATK RNAseq short variant discovery 4.2.0.0 workflow, which represents a CWL implementation of the official GATK best practices workflow given in WDL for RNASeq variant discovery. Starting from an unmapped BAM file, the workflow performs alignment to the reference genome, followed by marking of duplicates, reassigning of mapping qualities, base recalibration, variant calling, and variant filtering.

NewRecently published apps

We have published 10 tools from the GRIDSS module software suite (toolkit) containing tools useful for the detection of genomic rearrangements:

• GRIDSS tool, a structural variation caller for Illumina sequencing data. It calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence.
• GRIDSS Extract Overlapping Fragments is used to extract reads of interest for targeted GRIDSS variant calling.
• GRIDSS Annotate VCF Kraken2 adds Kraken2 classifications to single breakend and breakpoint inserted sequences.
• GRIDSS Annotate VCF RepeatMasker adds RepeatMasker classifications to inserted sequences.
• GRIDSS GeneratePonBedpe aggregates variants from multiple VCFs and counts the number of samples supporting each.
• GRIDSS SetupReference is used for generating additional files for the reference needed for running GRIDSS.
• GRIDSS Somatic Filter filters somatic calls from a VCF generated by GRIDSS joint tumor/normal variant calling.
• GRIDSS VIRUSBreakend is a high-speed viral integration detection tool. It is designed to be incorporated in the WGS pipelines with minimal additional cost.
• GRIPSS applies a set of filtering and post processing steps on GRIDSS paired tumor-normal output. It produces a high confidence set of somatic SV for a tumor sample.
• GRIPSS Hard Filter applies a set of filtering and post processing steps on GRIDSS paired tumor-normal output. It produces a high confidence set of somatic SV for a tumor sample.

Recently published apps

We’ve just published OlinkAnalyze DE, a tool that performs differential expression analysis on Olink Normalized Protein eXpression (NPX) data, and OlinkAnalyze QC that generates a quality control and exploratory analysis report on Olink NPX data.

SBFS support for macFUSE 4.x

SBFS is a command-line tool which enables interaction with Platform project files that are mounted as a local file system. In order to use SBFS, it is necessary to have the FUSE component installed. While FUSE is a part of the Linux kernel, on macOS it is necessary to install FUSE for macOS (which is now called macFUSE) and we are now adding support for macFUSE version 4.x (macFUSE 4.0.0 was released in October 2020, and that is when the name was changed from “FUSE for macOS” to “macFUSE”, while its latest version is macFUSE 4.2.4). Please note that SBFS is available as a BETA tool. Also, it’s not available for the Windows operating system, but only for Linux and macOS.

Data throughput usage dashboard now available for Enterprise

As an Enterprise Administrator or Division Administrator, you are able to review the data throughput either for the whole Enterprise or for individual divisions and for the desired time interval (e.g. weeks or months or the whole year). Files used in tasks, files used in Data Cruncher analyses and data downloads are included in the Data Throughput calculation.

As of January 1st 2022, Data Throughput only takes into account files that are used by the tools in a task (as opposed to files set as inputs to a task). Furthermore, data downloaded from the Internet by tasks and Data Cruncher analyses is also included in the calculation. Learn more about reviewing Enterprise data throughput.

Data Cruncher default environment update

The default environment for Data Cruncher interactive analyses has been updated to include more up-to-date versions of Python (upgraded to 3.9) and R (upgraded to 4.1). 

GDC Datasets version update

As of December 17, GDC datasets available through the Data Browser and the API correspond to GDC Data Release 30.0.

Recently published apps

• GRIDSS/PURPLE/LINX Workflow, used for somatic genomic rearrangement detection and classification on WGS data. This workflow takes a pair of matched tumor/normal BAM files and produces allele-specific copy number of every base of the genome, overall sample purity and ploidy, annotated SV clusters and gene fusion predictions. Moreover, it outputs detailed visualisations of the rearrangements in the tumor genome via integrated Circos plots showing copy number changes, clustered SVs, derivative chromosome predictions and impacted genes.
• PURPLE CNV Calling Workflow, used for somatic CNV calling and purity and ploidy estimation on WGS data. It is based on PURPLE 2.51, and consists of two additional tools – AMBER and COBALT. The workflow first calculates B-allele frequency (BAF) with AMBER and read depth ratios with COBALT, which is then used by PURPLE to estimate the purity, ploidy and copy number profile of a tumor sample.

Metadata editing using manifest files just got easier

Seven Bridges Platform provides the capability to modify metadata for multiple files in a project by using the Export metadata manifest and Edit metadata with manifest options in the File Browser. This release brings some major improvements to this feature:

• Support for different manifest file formats. Besides CSV, we have added support for the TSV file format.
• Use either file name or ID to identify a file. Files whose metadata is being edited can be specified using only file ID or file name (along with path) in the manifest file used with the Edit metadata with manifest option.
• Support for folders. The name column can contain file path within the project (along with the file name) if the file is in a folder instead of the project root.
• Better file naming and placement. A manifest file generated using the Export metadata manifest action is named in a user-friendly manner, in the manifest__YYYYMMDD_HHMMSS format. Also, an exported manifest file is generated in the project and made available as any other Platform file, meaning it can be downloaded, copied into another project, used in a task, etc.
• Added file size info. Manifest files exported via the Export metadata manifest option now contain file size information.
• Handling of non-standard characters. It is possible to have a comma or tab (or any other character) in a manifest file used with the Edit metadata with manifest option. Similarly, these characters will be properly formatted in a manifest file generated by the Export metadata manifest action.

Learn more:

• Edit metadata using the visual interface
• Metadata manifest file format

Recently published apps

We have just published and upgraded versions (from 2.17 to 2.22) of minimap2, a sequence alignment program that aligns DNA or mRNA sequences against a reference database, and minimap2 build index, a reference indexer for minimap2 aligner.

This week’s publishing streak also includes METAL, a tool for meta-analysis genome-wide association scans. METAL can combine either (a) test statistics and standard errors or (b) p-values across studies (taking sample size and direction of effect into account). A METAL analysis is a convenient alternative to a direct analysis of merged data from multiple studies.

Recently published apps

We have just published Picard FastqToSam, a tool that converts FASTQ files to an unaligned SAM or BAM file, and a set of seven Delly tools:

• Delly CNV for calling copy-number variants
• Delly Call, a structural variants caller
• Delly LR, a structural variants caller for long reads data
• Delly Sansa Annotate for annotating structural variants
• Delly Classify for classifying somatic or germline copy-number variants
• Delly Filter, a tool that filters structural variants
• Delly Merge for merging of structural variants in BCF format

Recently published apps

We have just published the following apps:

• CrossMap, a tool that converts genomic coordinates between different assemblies, and CrossMap Viewchain that prints the chain file for two assemblies in a human-readable format.
• VerifyBamID2 that estimates contamination of DNA samples from read data, accounting for ancestry information.