cifjoin [-l lane] [-t tile] run-folder

cifjoin --help

cifjoin --licence


Within a run folder, the intensity data for each cycle is stored in a separate CIF file so each file contains one cycle of one tile of one lane. Given a lane, tile and run folder, cifjoin merges the appropriate CIF files into a single CIF file containing all cycles which is appropriate for use with base calling software. The resulting CIF file is written to stdout.

-l, --lane [default: 4]

Lane of tile to create full CIF file.

-t, --tile [default: 33]

Tile number to create full CIF file of.

-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), cifsplit(1), int2cif(1)