Sailish is a software tool that implements a novel, alignment-free algorithm for the estimation of isoform abundances directly from a set of reference sequences and RNA-seq reads.  Rather than working at the read level, the fundamental unit of transcript coverage in Sailfish is the k-mer. Implementing this alternative, lightweight, approach allows Sailfish to dispense with many of the complexities of read mapping while remaining robust to sequencing errors. By replacing read mapping with intelligent k-mer indexing and counting, Sailfish is able to quantify isoform abundance orders of magnitude faster than existing tools.


  • Sailfish web site
  • Rob Patro, Stephen M. Mount, and Carl Kingsford (2014) 
    Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nature Biotechnology (doi:10.1038/nbt.2862)


Usage on Bridges


To see what other modules are needed, what commands are available and how to get additional help type

module help sailfish

To see what versions of Sailfish are available type

module avail sailfish

To use BLASR, include a command like this in your batch script or interactive session to load the BLASR module:

module load sailfish

Be sure to also load any other modules needed, as listed by the module help sailfish command.