Provided by: ssake_3.8.1-1_all
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)