Release note 10.09.23

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.