DeSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index.
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ABSTRACT:
SUBMITTER: Liu B
PROVIDER: S-EPMC6913027 | biostudies-literature | 2019 Dec
REPOSITORIES: biostudies-literature
Publications
deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index.
Liu Bo B Liu Yadong Y Li Junyi J Guo Hongzhe H Zang Tianyi T Wang Yadong Y
Genome biology 20191216 1
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. Benchm ...[more]
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