Program gto_fastq_minimum_quality_score

The gto_fastq_minimum_quality_score discards reads with average quality-score below of the defined.

For help type:

./gto_fastq_minimum_quality_score -h

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

Input parameters

The gto_fastq_minimum_quality_score 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_minimum_quality_score [options] [[--] args]
or: ./gto_fastq_minimum_quality_score [options]

It discards reads with average quality-score below value.

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

Basic options
-m, --min= The minimum average quality-score (Value 25 or 30 is commonly used)
< input.fastq Input FASTQ file format (stdin)
> output.fastq Output FASTQ file format (stdout)

Example: ./gto_fastq_minimum_quality_score -m < input.fastq > output.fastq

Console output example:

Total reads : value
Filtered reads : 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_minimum_quality_score program is a set of all the filtered FASTQ reads, followed by the execution report.

Using the input above with the minimum averge value as 30, an output example for this is the following:

@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72
Total reads : 2
Filtered reads : 1