The gto_fastq_quality_score_info analyses the quality-scores of a FASTQ file.
For help type:
./gto_fastq_quality_score_info -h
In the following subsections, we explain the input and output paramters.
The gto_fastq_quality_score_info 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_info [options] [[--] args]
or: ./gto_fastq_quality_score_info [options]
It analyses the 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 lenght of the maximum window
Example: ./gto_fastq_quality_score_info -m < input.fastq > output
Output example :
Total reads : value
Max read length : value
Min read length : value
Min QS value : value
Max QS value : value
QS range : value
An example of such an input file is:
@111 071112_SLXA-EAS1_s_7:5:1:817:345 length=72 1
GNNTGATGGCCGCTGCCGATGGCGNANAATCCCACCAANATACCCTTAACAACTTAAGGGTTNTCAAATAGA
+111
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9ICIIIIIIIIIIIIIIIIIIIIDIIIIIII>IIIIII/
@222 071112_SLXA-EAS1_s_7:5:1:801:338 length=72 2
NTTCAGGGATACGACGNTTGTATTTTAAGAATCTGNAGCAGAAGTCGATGATAATACGCGNCGTTTTATCAN
+222
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBIIIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I
The output of the gto_fastq_quality_score_info program is a set of information related to the file read.
Using the input above with the max window value as 30, an output example for this is the following:
Total reads : 2
Max read length : 72
Min read length : 72
Min QS value : 41
Max QS value : 73
QS range : 33
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 73 73 73 73 73 73 73 73 73 73 73 73 73 73 73 73 73 73