Release notes

November 27th, 2023

Single and Global logout flows defined by SAML protocol are now available for SSO  

Users who access the Seven Bridges Platform through Single Sign-On (SSO) can now perform Single (IdP Initiated) logout to log out of multiple SSO sessions, in a single click. Also, it is now possible to initiate Global (SP initiated) logout flow from the Seven Bridges Platform.

Recently published apps  

We have published the following tools in our Public Apps gallery:  

  • Tximport, a tool that imports and summarizes transcript-level estimates for transcript and gene-level analysis based on the tximport R/Bioconductor package. It is designed to simplify the import of transcript-level abundances, estimated counts, and effective lengths from a variety of upstream tools, for downstream transcript-level or gene-level analysis.  

Three tools from the SplAdder (3.0.4) toolkit:  

  • SplAdder build constructs splicing graphs and extracts alternative splicing events.  
  • SplAdder test differentially tests the usage of alternative event between two groups of samples.  
  • SplAdder viz generates visual overviews of splicing graphs and alternative events. SplAdder viz uses results generated by SplAdder build or SplAdder test to create plots.  

Five tools from the Qualimap 2.3 toolkit:  

  • Qualimap Multi-sample BAM QC reports QC metrics computed in BAM QC analysis combined for multiple samples.  
  • Qualimap Compute counts calculates how many reads are mapped to each region of interest.  
  • Qualimap RNA-seq QC reports quality control metrics and bias estimations for whole transcriptome sequencing.  
  • Qualimap Counts QC analyzes count data to assess a differential expression between two or more conditions.  
  • Qualimap BAM QC reports information for the evaluation of the quality of the provided alignment data.  

Six tools from the RSeQC 5.0.1 toolkit:  

  • RSeQC read distribution calculates how mapped reads were distributed over genomic features.  
  • RSeQC junction annotation compares detected splice junctions to the reference gene model.  
  • RSeQC inner distance is used to calculate the inner distance (or insert size) between two paired RNA reads.  
  • RSeQC infer experiment is designed to estimate how RNA-seq data is configured.  
  • RSeQC read duplication calculates read duplication rate determined by mapping position or sequence of the read.  
  • RSeQC bam stat summarizes mapping statistics of the provided alignment file.  

The Tidyproteomics 1.5.2 toolkit:  

  • Expression analysis – used for proteomics differential expression analysis.  
  • Data input and summary – used for loading protein or peptide data.  
  • Data subsetting and summary – used for subsetting protein or peptide data.  
  • Abundance normalization – used for abundance normalization of the protein or peptide data.  
  • Enrichment analysis – used for enrichment analysis after differential expression analysis.  
  • Annotate data – used for proteomics data annotation before enrichment analysis.  

Improved storage cost breakdown  

To meet the need for precise allocation of storage costs within a division, we have implemented a solution that enables precise per-project storage breakdown on the Seven Bridges Platform.  

The new solution includes improved accuracy in per-project storage breakdown, facilitating precise cost allocation, as well as elimination of storage size discrepancies between per-project and per-division calculations. This presents a great benefit both for users with administrative roles in divisions and Platform users in general as it increases transparency and provides a better insight into storage cost distribution.  

Recently updated apps  

TopHat2, a tool that aligns RNA-Seq reads to a genome to identify exon-exon splice junctions, just got updated to version 2.2.1 and upgraded to CWL version 1.2 (was previously available in CWL draft-2).

Read more

November 13th, 2023

Improved error messages for volume imports

To provide you with more detailed information about each import from an attached volume and enable you to resolve import issues independently, we have added improved notifications in the recently implemented Activity center, available by clicking Open activity center in the Activity feed. When any of the items from a particular import fails, you will be able to see an error message and a corresponding error code for each of the items, allowing you to understand and try to fix the issue. Furthermore, a description and link to the relevant documentation will be provided for each import from a volume.

Recently published apps

The Change-O 1.3.0 toolkit is the latest new toolkit addition in our Public Apps gallery. It includes the following apps: 

  • DefineClones  assigns Ig sequences into clonal groups. 
  • BuildTrees – creates IgPhyML input files. 
  • ParseDb – parses and updates input database files. 
  • AlignRecords – multiple aligns sequence fields. 
  • AssignGenes – assigns V(D)J gene annotations. 
  • MakeDb – creates standardized databases output from the input germline alignment results. 
  • CreateGermlines – reconstructs germline V(D)J sequences for alignment data. 
  • ConvertDb – parses input tab-delimited database files and converts them to different output formats. 

Recently updated apps

We updated Broad Institute’s best practices for somatic copy number variant discovery analyses, to version in our Public Apps gallery: 

  • GATK Somatic CNV Panel Workflow – used for creating a panel of normals (PON) given a set of normal samples. 
  • GATK Somatic CNV Pair Workflow – used for detecting copy number variants (CNVs) from WES/WGS single sample data in tumor-only or matched-normal mode. 
Read more

October 30th, 2023

Recently published apps

The pRESTO 0.7.1. toolkit is the latest new toolkit addition in our Public Apps gallery. It includes the following apps: 

  • ParseLog  Parses pRESTO log records and outputs values in TAB-separated tables. 
  • BuildConsensus – Builds consensus sequences. 
  • ClusterSets – Clusters sequences into groups. 
  • CollapseSeq– Removes duplicates sequences from input FASTA/FASTQ files. 
  • PairSeq – Sorts and matches sequences across input files. 
  • ConvertHeaders – Converts sequence headers to pRESTO format. 
  • AlignSets – Aligns sequences using different methods. 
  • FilterSeq – Filters input sequences. 
  • ParseHeaders – Manipulates sequence headers. 
  • SplitSeq – Splits and samples sequence files. 
  • UnifyHeaders – Reassigns or deletes sequence header fields. 
  • AssemblePairs – Assembles paired-end reads to a single sequence. 
  • MaskPrimers – Removes primers and annotates sequences with primers and barcodes. 
  • EstimateError – Estimates annotation set error rates.  

We also published the following new tools: 

  • ComBat-seq (sva 3.35.2), an R tool used for batch effect adjustment in bulk RNA-seq data. Some additional improvements to the tool wrapper were developed, like removing more than one batch by dataset and adapting outputs to be compatible with downstream analyses (DeSeq). 
  • GffRead (0.12.7) GFF/GTF utility tool providing format conversions, filtering, FASTA sequence extraction, and more. 

Recently updated apps

We published the following updates in our Public Apps gallery: 

  • RNA-seq alignment – STAR (2.7.10a), a workflow that performs the first step of RNA-seq analysis – alignment of the reads to a reference genome. It is used to generate aligned BAM files (in genome and transcriptome coordinates) from RNA-seq data, which can later be used in further RNA studies, like gene expression analysis. 
  • Trim Galore! (0.6.10) is a wrapper around adapter trimming and quality control tools Cutadapt and FastQC with extra functionality for RRBS data.
Read more

October 9th, 2023

Data Browser on the Seven Bridges Platform deprecated to promote interoperability with the CGC  

As the next step in promoting interoperability, we deprecated the Data Browser on the Seven Bridges Platform. As Data Browser remains available on the CGC, this will help promote the CGC as the hub for publicly available data and enable Seven Bridges Platform users who have a CGC account to discover all datasets that are available in the Data Browser on the CGC and much more. 

To complete the process of Data Browser deprecation, in the upcoming period we will disable access to files that were previously imported using Data Browser.  

Recently published apps

 We published Immcantation toolkit 4.4.0 in our Public Apps gallery. The toolkit consists of a set of pipeline scripts which are wrapped as the following tools: 

  • preprocess-phix – removes reads which align to phiX174 from the input sequence file. 
  • presto-abseq – runs pRESTO tools for pre-processing of NEBNext / ABSeq immune sequencing data. 
  • presto-clontech – uses pRESTO tools for analyzing Takara Bio/Clontech SMARTer v1 immune sequencing kit data. 
  • presto-clontech-umi – uses pRESTO tools for analyzing Takara Bio/Clontech SMARTer v2 (UMI) immune sequencing kit data. 
  • changeo-10x – annotates and infers clonal relationships in Cell Ranger 10x Genomics single-cell V(D)J data. 
  • changeo-igblast – does V(D)J alignment using IgBLAST. 
  • tigger-genotype – does TIgGER polymorphism detection and genotyping. 
  • shazam-threshold – calculates clonal assignment threshold. 
  • changeo-clone – runs Change-O cloning and germline reconstruction. 

We also published Nirvana 3.18.1. Nirvana annotates variants from VCF file input and generates a JSON file with results. 

Read more

September 25th, 2023

Recently published apps

We published the following apps in our Public Apps gallery:

  • RNA-SeQC 2.4.2, a tool that computes post-alignment quality control metrics for RNA-Seq data. It takes aligned reads in BAM/SAM or CRAM format and an annotation file as inputs, and outputs different alignment metrics files
  • scCODA 0.1.9, a Python-based tool that performs differential analysis of cell populations.
Read more

September 20th, 2023

Recently published apps

We have just published the following tools from the BBTools 39.01 toolkit:

  • BBDuk: used for trimming, filtering, and masking of input reads.
  • Reformat: used for generic read-processing tasks (changing ASCII quality encoding, interleaving, file format, compression).
  • BBMap: used for splice-aware read alignment.
  • Dedupe: used for removing duplicates from input sequences.
  • SplitNextera: used for splitting Nextera long-mate-pair reads.
  • CalcUniqueness: used for determining library complexity and the need for additional sequencing by generating kmer uniqueness histogram.
  • Taxonomy: used for printing taxonomy information for provided organism identifiers.
  • Repair: used to correct disordered reads and reads whose mates have been lost.
  • Seal: used for alignment-free sequence quantification.
  • BBMerge: used for merging overlapping paired end reads.
  • BBMask: used for masking low-complexity, tandem repeats or SAM mapped regions.
  • Tadpole: used as a kmer-based assembler.
  • Statistics: used for calculating assembly statistics.
  • BBNorm: used for normalizing read depth based on kmer counts.
Read more

September 4th, 2023

NewDRS notification improvements and the brand new Activity center

To provide you with more detailed information about each DRS import operation and enable you to resolve import issues independently, we have improved DRS-related notifications and implemented the Activity center, available by clicking Open activity center in the Activity feed. When any of the items from a particular DRS import fail, you will be able to see an error message and a corresponding error code for each of the items, allowing you to understand and try to fix the issue. Furthermore, a description and link to the relevant documentation will be provided for each import from a DRS server.

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August 16th, 2023

NewFile download restriction can now be activated for project files

To further improve security controls over data available on the Seven Bridges Platform, we have implemented the option to restrict downloading of files from platform projects. The restriction is  enabled per project, on project creation, along with optional parameters that prevent downloading of analysis output files and allow file copies to be present in other projects. Learn more about download restrictions.

This functionality is not available by default. To learn what your options are and have it enabled, please get in touch with your Velsera contact person or

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August 7th, 2023

Recently published apps

We have just published RTG Tools 3.12.1 (ROCPlot, VCFEval, Format), MaxQuant and GATK GenotypeGVCFs tools:

  • RTG Tools Format converts data files from FASTA/FASTQ/SAM/BAM into the RTG Sequence Data File (SDF) format.
  • RTG Tools VCFEval is a tool that performs sophisticated comparison of VCF files.
  • RTG Tools ROCPlot is used to plot ROC curves from ROC data files generated by RTG Tools VCFEval.
  • MaxQuant integrates algorithms specifically developed for high-resolution, quantitative MS data, and it is applicable for shotgun proteomics.
  • GATK GenotypeGVCFs is used to joint-genotype GVCF files created by GATK HaplotypeCaller/GATK GenomicsDBImport tools.
Read more

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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