RT Journal Article
SR Electronic
T1 deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 612176
DO 10.1101/612176
A1 Bo Liu
A1 Yadong Liu
A1 Junyi Li
A1 Hongzhe Guo
A1 Tianyi Zang
A1 Yadong Wang
YR 2019
UL http://biorxiv.org/content/early/2019/10/15/612176.abstract
AB Long-read RNA sequencing (RNA-seq) is promising to transcriptomics studies, however, the alignment of long RNA-seq reads is still non-trivial due to high sequencing errors and complicated gene structures. Herein, we propose deSALT, a tailored two-pass alignment approach, which constructs graph-based alignment skeletons to infer exons and uses them to generate spliced reference sequences to produce refined alignments. deSALT addresses several difficult technical issues, such as small exons and sequencing errors, which breakthroughs the bottlenecks of long RNA-seq read alignment. Benchmarks demonstrate that deSALT has a greater ability to produce accurate and homogeneous full-length alignments. deSALT is available at: https://github.com/hitbc/deSALT.