tqs1

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.