Systematic evaluation of spliced alignment programs for RNA-seq data

Authors compare RNA-seq aligners on mouse and human data sets using benchmarks such as alignment yield, splice junction accuracy and suitability for transcript reconstruction. The work highlights the strength of each program and discusses outstanding needs in RNA-seq analysis. High-throughput RNA sequencing is an increasingly accessible method for studying gene structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the alignment of partial transcript reads to a reference genome sequence. To assess the performance of current mapping software, we invited developers of RNA-seq aligners to process four large human and mouse RNA-seq data sets. In total, we compared 26 mapping…

• WT
  Wellcome Trust
• EM
  European Molecular Biology Laboratory
• NI
  National Institutes of Health
• NH
  National Human Genome Research Institute

  Award: U54HG004555