Accurate spliced alignment of long RNAsequencing reads

Abstract

Long-read RNA sequencing techniques are establishing themselves as the primary sequencing technique to study the transcriptome landscape. Many such analyses are dependent on read alignments. However, the error rate and sequencing length of long-read technologies create new challenges for accurately aligning these reads. We present an alignment method uLTRA based on a novel two-pass collinear chaining algorithm. Furthermore, uLTRA can be used both as a stand-alone aligner and as a wrapper around minimap2 for improved alignments in gene regions. We show that uLTRA produces higher accuracy over state-of-the-art aligners with substantially higher accuracy for small exons on simulated and synthetic data. On biological data where true read location is unknown, we show several examples where uLTRA aligns to known and novel isoforms with exon structures that are not detected with other aligners. uLTRA is available at https://github.com/ksahlin/ultra.