debian man page for tqs

TQS(1)							      General Commands Manual							    TQS(1)

NAME
       tqs - Trim Quality Solexa-Illumina Sequences

SYNOPSIS
       Quality trim solexa-Illumina sequence reads using user-defined thresholds.

OPTIONS
       -h, --help
		 show this help message and exit

       -f SEQFILE, --sequence file=SEQFILE
		 Illumina sequence file - Output format from the 1G Genome Analyzer (_seq.txt):
		     7	     1	     255     669
		     AACCCCCACTCCTACAACGCCATCATTCCCCTCGAC

       -q QUALFILE, --qual file=QUALFILE
		 A prb file containing all the Illumina intensities, as outputted by the 1G Genome Analyzer (_prb.txt)

       -l MER, --length=MER
		 Length of sequence reads (i.e. Number of sequencing cycles, default=36)

       -t THRESHOLD, --threshold=THRESHOLD
		 Base intensity threshold value (-40 to 40, default=5)

       -d DIFF, --difference=DIFF
		 Base intensity difference between top intensity and second best (1 to 80, default=5)

       -c CONSEC, --consec=CONSEC
		 Minimum number of consecutive bases passing threshold values (default=20)

       -v, --verbose
		 Runs in Verbose mode.

SEE ALSO
       /usr/share/doc/ssake/TQS.readme

AUTHORS
       This  manual page was written by Andreas Tille <tille@debian.org> for the Debian system (but may be used by others).  Permission is granted
       to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by
       the Free Software Foundation.

       On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.

								   January 2008 							    TQS(1)