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Release note 04.08.24

9 months ago by Marko Marinkovic

Recently published apps 

Here are the new apps published in our Public Apps gallery: 

  • ASCAT 3.1.2 tools (ASCAT prepareTargetedSeq, ASCAT prepareHTS and ASCAT). ASCAT prepareTargetedSeq prepares SNP references for ASCAT processing of targeted sequencing data. ASCAT prepareHTS prepares sequencing data (WGS, WES or targeted) for ASCAT. ASCAT infers tumor ploidy, purity and allele-specific copy number profiles. 
  • JAFFAL 2.3 tool. JAFFAL is used to detect fusion genes from long-read (PacBio and ONT) transcriptome sequencing with high accuracy, overcoming the challenges posed by higher error rates in long-read data. 
  • Ballgown 2.34.0 toolkit. Ballgown is a package designed to facilitate flexible differential expression analysis of RNA-Seq data. It also provides functions to organize, visualize, and analyze the expression measurements for transcriptome assembly 

Apps with version updates 

StringTie 2.2.1 toolkit. StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. StringTie Merge tool merges/assembles GTF/GFF transcript files into a non-redundant set of transcripts. This tool should be used after StringTie transcript assembling of each sample in the experiment.