Release note 05.04.22

Recently published apps

We have just published the following apps:

  • An updated version of the SRA Download and Set Metadata workflow (SRA Toolkit 3.0.0) that downloads metadata associated with SRA accession via SRA Run Info CGI, (on-demand instance) FASTQ files and sets corresponding metadata.
  • OptiType (v1.3.5, CWL1.2), a tool designed for precision HLA typing from next-generation sequencing data. It is based on the assumption that the correct HLA genotype explains the highest number of mapped reads. Therefore, it searches for the best HLA allele combination of up to six major and six minor HLA-I alleles. The maximum number of reads potentially originating from one selection under the biological constraints that at least one and at most two alleles are selected per locus can be conveniently formulated as an ILP.
  • fastENLOC (v1.0, CWL1.2), a tool that enables integrative genetic association analysis of molecular QTL data and GWAS data. It performs integration of the results from molecular quantitative trait loci (QTL) mapping into genome-wide genetic association analysis of complex traits, with the primary objective of quantitatively assessing the enrichment of the molecular QTLs in complex trait-associated genetic variants and the colocalizations of the two types of association signals.