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.