Release notes

January 31st, 2022

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.

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January 17th, 2022

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.

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December 27th, 2021

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.

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December 17th, 2021

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.
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December 6th, 2021

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:

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.

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November 29th, 2021

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
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November 8th, 2021

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.
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November 1st, 2021

Recently published apps

We have just published DRAGMAP, the open source DRAGEN mapper/aligner that can be used to align single or paired-end reads (FASTQ) or an input BAM file. The app is available in the Public Apps gallery.

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October 25th, 2021

Recently published apps

We have just updated the content of our public app galleries with new GATK releases:

  • GATK Pre-Processing For Variant Discovery workflow is used to prepare data for variant calling analysis. The workflow consists of two major segments: alignment to reference genome and data cleanup operations that correct technical biases. Resulting BAM files are ready for variant calling analysis and can be further processed by other BROAD best practice pipelines, like Generic Germline Short Variant Per-Sample Calling workflow, Somatic CNVs workflow, and Somatic SNVs + INDELs workflow.
  • GATK Generic Germline Short Variant Per-Sample Calling workflow that calls germline variants in a WGS sample with GATK HaplotypeCaller, starting from an analysis-ready BAM file.

And six GATK tools:

  • GATK GatherBQSRReports tool that gathers scattered BQSR recalibration reports into a single file.
  • GATK BaseRecalibrator tool that generates a recalibration table based on various covariates for input mapped read data.
  • GATK ApplyBQSR tool that recalibrates the base quality scores of an input BAM or CRAM file containing reads.
  • GATK HaplotypeCaller tool for calling germline SNPs and indels from input BAM file(s) via local re-assembly of haplotypes.
  • GATK VariantFiltration tool used for filtering variants in a VCF file based on INFO and/or FORMAT annotations.
  • GATK MergeVcfs, used for combining multiple variant files.
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We are always engaged in research and development, working to build the future of genomics, science, and health. Let's work together. We'd love to hear about your projects and challenges, so drop us a line.

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