cifsplit [-o offset] [-s suffix] file

cifsplit --help

cifsplit --licence


Split a CIF file containing intensity data from the Illumina sequencing platform into two CIF files, the first containing cycles 1 to offset (default offset being half the number of cycles) and the second containing the remaining cycles. Examples where this is useful include the common case where a run was paired end and it is desirable to look at the ends separately, and more exotic cases like TRADIS data where the first few cycles are all from the same template and so not interesting.

If no file is given on the commandline, cifsplit reads from stdin.

-o, --offset offset [default: half number of cycles of file]

Offset of second read in paired-end file. Run is split into two at this offset, so pairs do not have to have equal length. The default is to split the read equally in two.

-s, --suffix suffix [default: "_end"]

Suffix which to add to names to identify pairs. The original file "s_4_33.cif" will have pairs "s_4_33_end1.cif" and "s_4_33_end2.cif" by default. If the read was read from stdin, pairs are written to "intensities_end1.cif" and "intensities_end2.cif"

-h, --help

Display information about usage and exit.


Display licence terms and exit.


Written by Tim Massingham,



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.


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