Exon

Combinatorics

De Bruijn sequence

Homogeneous

Computer science

Gene

Graph

Mathematics

Biology

Genetics

Computational biology

Theoretical computer science

De Bruijn graph

Genome biology

The alignment of long-read RNA sequencing reads is non-trivial due to high sequencing errors and complicated gene structures. 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 break through 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.

deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index