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deSALT website  

deSALT(de Bruijn graph-based Spliced Aligner for Long Transcriptome reads) is a novel alignment approach with faster speed and sensitive exon identification. Taking the advantages of its novel two pass alignment strategy based on de Bruijn graph-based index, efficient alignment skeleton generation, sensitive exon identification and specifically designed local alignment, deSALT is a fast and accurate RNA-seq long read alignment approach. It has ability to produce high quality full-length read alignment, which is effective to recover the exons and splicing junctions along the entire reads.

Environment Modules

Run module spider deSALT to find out what environment modules are available for this application.

System Variables

  • HPC_DESALT_DIR - installation directory
  • HPC_DESALT_BIN - executable directory


If you publish research that uses deSALT you have to cite it as follows:

Liu, B., Liu, Y., Li, J. et al. deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index. Genome Biol 20, 274 (2019) doi:10.1186/s13059-019-1895-9