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Release note

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.