The gto_fastq_quality_score_max analyses the maximal quality-scores of a FASTQ file.
For help type:
./gto_fastq_quality_score_max -h
In the following subsections, we explain the input and output paramters.
The gto_fastq_quality_score_max program needs two streams for the computation, namely the input and output standard. The input stream is a FASTQ file.
The attribution is given according to:
Usage: ./gto_fastq_quality_score_max [options] [[--] args]
or: ./gto_fastq_quality_score_max [options]
It analyses the maximal quality-scores of a FASTQ file.
-h, --help show this help message and exit
Basic options
< input.fastq Input FASTQ file format (stdin)
> output Output read information (stdout)
Optional
-m, --max= The maximum window length (default 40)
Example: ./gto_fastq_quality_score_max -m < input.fastq > output
An example of such an input file is:
@111 071112_SLXA-EAS1_s_7:5:1:817:345 length=72 1
GNNTGATGGCCGCTGCCGATGGCGNANAATCCCACCAANATACCCTTAACAACTTAAGGGTTNTCAAATAGA
+
IIIIIIIIIIII9IG9ICIIIIIIIIIIIABAAABCIIIIFFGIIAACBBIIIII6IBIIIIIII>IIIIII/
@222 071112_SLXA-EAS1_s_7:5:1:801:338 length=72 2
NTTCAGGGATACGACGNTTGTATTTTAAGAATCTGNAGCAGAAGTCGATGATAATACGCGNCGTTTTATCAN
+
IIIIIIIABAAABCIIIIFFGIIAACBBIIIII6IBIIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I
The output of the gto_fastq_quality_score_max program is a set of information related to the file read, considering the maximal quality scores.
Using the input above with the max window value as 30, an output example for this is the following:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+
73 73 73 73 73 73 73 73 73 73 73 73 66 73 73 73 73 73 73 73 73 73 73 73 73 73 73 73 73 73