RT Journal Article
SR Electronic
T1 Accurate spliced alignment of long RNA sequencing reads
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.09.02.279208
DO 10.1101/2020.09.02.279208
A1 Kristoffer Sahlin
A1 Veli Mäkinen
YR 2020
UL http://biorxiv.org/content/early/2020/09/03/2020.09.02.279208.abstract
AB Long-read RNA sequencing techniques are quickly establishing themselves as the primary sequencing technique to study the transcriptome landscape. Many such analyses are dependent upon splice alignment of reads to the genome. 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 that, on simulated and synthetic data, shows higher accuracy over state-of-the-art with substantially higher accuracy for small exons. We show several examples on biological data 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.Competing Interest StatementThe authors have declared no competing interest.