tqs(1) Trim Quality Solexa-Illumina Sequences


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


-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
-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)
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.


This manual page was written by Andreas Tille <[email protected]> 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.