deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index
deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index
Abstract 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.
Liu Bo、Liu Yadong、Zang Tianyi、Wang Yadong、Guo Hongzhe、Li Junyi
Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of TechnologyCenter for Bioinformatics, School of Computer Science and Technology, Harbin Institute of TechnologyCenter for Bioinformatics, School of Computer Science and Technology, Harbin Institute of TechnologyCenter for Bioinformatics, School of Computer Science and Technology, Harbin Institute of TechnologyCenter for Bioinformatics, School of Computer Science and Technology, Harbin Institute of TechnologyCenter for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology
生物科学研究方法、生物科学研究技术分子生物学生物工程学
long read alignmentRNA-seqde Bruijn graph-based index
Liu Bo,Liu Yadong,Zang Tianyi,Wang Yadong,Guo Hongzhe,Li Junyi.deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index[EB/OL].(2025-03-28)[2025-06-08].https://www.biorxiv.org/content/10.1101/612176.点此复制
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