We are using Wings to execute workflows for Next Generation Sequencing data. The diagram shows a workflow for processing mRNA-Seq data, which performs seven alignment steps (genome, junction, fusion, polyA, polyT, miR, and paired) in the analysis. The workflow completes expression measures for each gene, exon, and splice form from a given set of samples. It also creates a bed-graph (for visualization in the UCSC genome browser), examines the reads for evidence of gene fusions, predicts changes in poly-adenylation and miRNA-binding sites, and also uses variant discovery algorithms to predict variants from the RNA-Seq data. Semantic constraint are used for error-checking and sample information propagation, such as verification of a sample’s sex from the genotyping output.