This is the command tqs that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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.
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