Release notes

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.

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.

Recently published apps

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

• GATK Pre-Processing For Variant Discovery 4.2.0.0 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 4.2.0.0 workflow that calls germline variants in a WGS sample with GATK HaplotypeCaller, starting from an analysis-ready BAM file.

And six GATK 4.2.0.0 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.

Recently published apps

We’ve just published four tools from the OncoGEMINI 1.0.0 toolkit:

• OncoGEMINI Bottleneck that identifies somatic variants with increasing allele frequency in longitudinal data.

• OncoGEMINI Loh, a command tool that performs loss of heterozygosity analysis.

• OncoGEMINI Truncal that recovers variants that appear in all tumor samples, but are absent in the normal sample.

• OncoGEMINI Unique tool for identifying somatic variants unique to a subset of samples.

Billing information just got more informative and organized

The following improvements have been made on the Billing page available to Enterprise and Division administrators:

• The Billing page has been redesigned and now consists of three sections: Billing information, Instance limits and Payment information.
• The start date from which costs are calculated is now displayed for the current billing period.
• Additional charges and credits information is now renamed to Charges and Refunds and grouped in the Additional subsection.
• Total Platform charges now sum up costs for Analysis, Storage and Additional charges.

Recently published apps

SBG Image Processing Toolkit 

SBG Image Processing Toolkit consists of apps that enable various stages of machine learning image processing. Seamless integration between the tools of this toolkit provides an easy and logical analysis flow, while enabling support of various data types, preprocessing steps and utilizing computation capabilities of the Seven Bridges Platform.

1. SBG Deep Learning Image Classification Exploratory Workflow is an image classifier pipeline that relies on the transfer learning approach. This allows the use of pre-trained models as the starting point for building a model adjusted to given image datasets. Furthermore, the pipeline allows training of the model for a variety of hyperparameter combinations in parallel by utilizing multiple GPU instances, while detailed metrics and visualizations help determine the best configuration that can later be used to make predictions on new data instances. 
2. SBG Deep Learning Prediction is an image classifier tool that classifies unlabeled images based on labeled data. It is intended as a final step after the SBG Deep Learning Image Classification Exploratory Workflow. Testing different configurations in parallel with the exploratory workflow and finding the best model configuration for the given dataset, then using SBG Deep Learning Prediction with that configuration and all available labeled images as the training data provides the optimal training conditions which lead to the best classification results.
3. SBG Histology Whole Slide Image Preprocessing takes SVS histopathology images, removes various artifacts, and outputs the desired number of best quality tiles in PNG format that consist of at least 90% tissue.
4. SBG X-Ray Image Preprocessing Workflow performs the selected X-ray image enhancement algorithm: unsharp masking (UM), high-frequency emphasis filtering (HEF) or contrast limited adaptive histogram equalization (CLAHE). 
5. SBG Stain Normalization involves casting an array of images in the stain colors of a target image. Stain normalization is used as a histopathology image preprocessing step to reduce the color and intensity variations present in stained images obtained from different laboratories.
6. SBG Medical Image Convert performs medical image format conversion. If the input data are medical images in a non-standard format (e.g. SVS, TIFF, DCM or DICOM), SBG Medical Image Convert converts them to PNG format.
   
7. SBG Split Folders organizes an image directory into the train and test subdirectory structure. These directories are necessary inputs for SBG Deep Learning Image Classification Exploratory Workflow and SBG Deep Learning Prediction.

HistoQC

HistoQC is an open-source quality control tool for digital pathology slides. It performs fast quality control to not only identify and delineate artefacts but also discover cohort-level outliers (e.g., slides stained darker or lighter than others in the cohort). It outputs an interactive user interface for easy viewing and understanding of the results.

Minimac4

Minimac4 is a genetic imputation algorithm that can be used to impute genotypes in a genomic region starting from a reference panel in M3VCF format and pre-phased target GWAS haplotypes.

BOLT-LMM

BOLT-LMM is a tool that tests the association between genotypes and phenotypes using a linear mixed model.