ciftools – utilities for manipulating CIF intensity files


ciftools is a collection of utilities for manipulating CIF format intensity files produced by the Illumina sequencing platform.
  • cifboot: Produce bootstrap replicates of intensity data.
  • cifcat: Concatencate several CIF files together.
  • cifinfo: Display information about a tile intensity data.
  • cifjoin: Join several CIF files from a run-folder together.
  • cifsplit: Split a CIF into two by cycle.
  • cifstat: Show basic statistics about cycles in a CIF file.
  • int2cif: Convert an old-style INTensity format file into CIF. file.


  • 30 Mar 2012.
    New utility cifstat to determine basic statistics about CIF files.
  • 29 Mar 2012.
    Fixes for when number of clusters is large.
  • 18 Nov 2010.
    New utility cifcat.
  • 05 Oct 2010.
    Initial release of source code.


The ciftools software package is freely available under the GNU General Public Licence version 3 (see for further information). A copy of the licence is provided with the software.

ciftools uses the optimised SFMT code for the Mersenne twister random number generator produced by Mutsuo Saito and Makoto Matsumotom, which is available from Hiroshima University under a three-clause BSD style licence.