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

Long-read RNA sequencing (RNA-seq) is a promising approach in transcriptomics studies, however, the alignment of the long reads is a fundamental but still non-trivial task due to sequencing errors and complicated gene structures. We propose de Bruijn graph-based Spliced Aligner for Long Transcriptome read (deSALT), a tailored two-pass long RNA-seq read alignment approach, which constructs graph-based alignment skeletons to sensitively infer exons and uses them to generate high-quality spliced reference sequences to produce refined alignments. deSALT addresses several difficult technical issues, such as small exons and serious sequencing errors, which breakthroughs the bottlenecks of long RNA-seq read alignment. Benchmarks demonstrate that this approach has a greater ability to produce accurate and homogeneous full-length alignments and thus has enormous potentials in transcriptomics studies.

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