Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

Nat Biotechnol. 2014 May;32(5):462-4. doi: 10.1038/nbt.2862. Epub 2014 Apr 20.


We introduce Sailfish, a computational method for quantifying the abundance of previously annotated RNA isoforms from RNA-seq data. Because Sailfish entirely avoids mapping reads, a time-consuming step in all current methods, it provides quantification estimates much faster than do existing approaches (typically 20 times faster) without loss of accuracy. By facilitating frequent reanalysis of data and reducing the need to optimize parameters, Sailfish exemplifies the potential of lightweight algorithms for efficiently processing sequencing reads.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Brain Chemistry
  • Computational Biology / methods*
  • Humans
  • Models, Biological
  • RNA Isoforms* / analysis
  • RNA Isoforms* / chemistry
  • RNA Isoforms* / genetics
  • Sequence Analysis, RNA / methods*
  • Software*


  • RNA Isoforms