cifboot [-b boot] [-n nsample] [-p prefix] [-s seed] file

cifboot --help

cifboot --licence


cifboot creates nonparametric bootstraps from a file containing intensity data in CIF format from an Illumina sequencing machine. If no file is specified, then cifboot reads from stdin. Unless otherwise specified, the bootstrap sets of data contain the same number of clusters as the original. Clusters are sampled uniformly with replace, so the same cluster can be chosen many times (the number of times each cluster is chosen being approximately Poisson distributed with mean one).

-b, --boot nboot [default: 100]

Number of bootstrap replicates to produce. Each replicate is written to its own file.

-n, --nsample nsample [default: number of clusters]

Number of clusters in each bootstrap. Default is the same as the number as the input file.

-p, --prefix prefix [default: "boot_"]

Prefix for bootstrap files. Output bootstrap files will be named prefixXXX.cif, where XXX is XXX’th bootstrap field-width chosen to accomodate maximum value.

-s, --seed seed [default: from clock]

Seed for random number generator.

-h, --help

Display information about usage and exit.


Display licence terms and exit.


Only an ordinary nonparametric bootstrap of the data is performed, so individual clusters may appear several times in the output. This behaviour is undesirable for some applications and there should probably be a whitening option to add a small amount of noise to the output, making each cluster unique.


Written by Tim Massingham,

cifboot 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.



Erfron, B. (1994) An Introduction to the Bootstrap. Chapman and Hall.


Copyright © 2010 European Bioinformatics Institute. Free use of this software is granted under the terms of the GNU General Public License (GPL). See the file COPYING in the ciftools distribution or for details.

The included SFMT library is copyright © 2006,2007 Mutsuo Saito, Makoto Matsumoto and Hiroshima University, and is distributed under a three-clause BSD style licence. Seee


ciftools(1), cifcat(1), cifinfo(1), cifjoin(1), cifsplit(1), int2cif(1)