Program gto_fastq_extract_quality_scores

The gto_fastq_extract_quality_scores extracts all the quality-scores from FASTQ reads.

For help type:

./gto_fastq_extract_quality_scores -h

In the following subsections, we explain the input and output paramters.

Input parameters

The gto_fastq_extract_quality_scores 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_extract_quality_scores [options] [[--] args]
or: ./gto_fastq_extract_quality_scores [options]

It extracts all the quality-scores from FASTQ reads.

-h, --help show this help message and exit

Basic options
< input.fastq Input FASTQ file format (stdin)
> output.fastq Output FASTQ file format (stdout)

Example: ./gto_fastq_extract_quality_scores < input.fastq > output.fastq

Console output example:

Total reads : value
Total Quality-Scores : value

An example of such an input file is:

@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72
+SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72
@SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72
+SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72


The output of the gto_fastq_extract_quality_scores program is a set of all the quality scores from the FASTQ reads, followed by the execution report.

The execution report only appears in the console.

Using the input above, an output example for this is the following:

Total reads : 2
Total Quality-Scores : 144