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

Bo Liu, Yadong Liu, Junyi Li, Hongzhe Guo, Tianyi Zang & Yadong Wang

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.

代表性项目

2018年启动我国首个,世界规模最大的健康人群基因组研究计划——中国十万人基因组计划。此计划旨在从我国七大主要区域选取十万中国参比人群样本,进行全基因组测序和PB级基因组大数据分析,构建世界最高精度的中国人基因组变异图谱,揭示中国人的基因密码,并发现中国人基因与环境、表型之间的重要关系,为健康中国建设奠定科学基础。中国十万人基因组计划获得央视新闻等多家中外媒体报道,在国际科学界产生巨大反响。