Program gto_fastq_minimum_local_quality_score_forward

The gto_fastq_minimum_local_quality_score_forward filters the reads considering the quality score average of a defined window size of bases.

For help type:

./gto_fastq_minimum_local_quality_score_forward -h

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

Input parameters

The gto_fastq_minimum_local_quality_score_forward 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_local_quality_score_forward [options] [[--] args]
or: ./gto_fastq_minimum_local_quality_score_forward [options]

It filters the reads considering the quality score average of a defined window size
of bases.

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

Basic options
-k, --windowsize= The window size of bases (default 5)
-w, --minavg= The minimum average of quality score (default 25)
-m, --minqs= The minimum value of the quality score (default 33)
< input.fastq Input FASTQ file format (stdin)
> output.fastq Output FASTQ file format (stdout)

Example: ./gto_fastq_minimum_local_quality_score_forward -k -w
-m < input.fastq > output.fastq

Console output example:
Minimum QS : value

Total reads : value
Trimmed 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_local_quality_score_forward program is a FASTQ file with the reads filtered following a quality score average of a defined window of bases.

The execution report only appears in the console.

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

Minimum QS : 33
@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
Total reads : 2
Trimmed reads : 1