
TQS

Trim Quality Solexa-Illumina Sequences (TQS)

SYNOPSIS
   Quality trim solexa-Illumina sequence reads using user-defined thresholds
"""
__author__ = "Rene L. Warren"
__version__ = '1.0'

#LICENSE
#   Copyright (c) 2007 Canada's Michael Smith Genome Science Centre.  All rights reserved.

#   This program is free software; you can redistribute it and/or
#   modify it under the terms of the GNU General Public License
#   as published by the Free Software Foundation; either version 2
#   of the License, or (at your option) any later version.

#   This program is distributed in the hope that it will be useful,
#   but WITHOUT ANY WARRANTY; without even the implied warranty of
#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#   GNU General Public License for more details.

Execution example
==================
python3 TQS.py -f test_seq.txt -q test_prb.txt -l 36 -t 5 -d 5 -c 20


Options
=======
python3 TQS.py --help

Usage: TQS.py [options]

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.


Output
======

.log file: Indicates the option chosen and tracks the execution time
.fa file: A single fasta file containing the sequence reads that passed the filter specified
