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SMRT is a tool for calling SNPs and assembling haplotypes based on long PacBio reads. It is not a de novo assembly tool and hence, this tool should not be confused with other tools offered as part of the SMRT suite of tools by PacBio developers. The name for this tool is based on Single Molecule Real Time (SMRT) sequencing and the paper describing this tool used PacBio reads. Essentially, it is a method that is able to use the more error prone long PacBio reads to call SNP and haplotypes whereas other methods may need to resort to the use of more accurate short reads for SNP calling.


Sequence analysis


  • Operation: Haplotype mapping
  • Software interface: Command-line user interface
  • Language: Java
  • Operating system: Linux; Mac OS X
  • License: Not stated
  • Cost: free
  • Version name: -
  • Credit: Research Grants Council of the Hong Kong Special Administrative Region, China; National Science Foundation of China; Tianjin Research Program of Application Foundation and Advanced Technology
  • Contact: cswangl _at_
  • Collection: -


Guo F, Wang D, Wang L "Progressive approach for SNP calling and haplotype assembly using single molecular sequencing data." Bioinformatics
PMID: 29474523

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