Program gto_fastq_minimum_local_quality_score_reverse

The gto_fastq_minimum_local_quality_score_reverse filters the reverse reads, considering the quality score average of a defined window size of bases.

For help type:


			  			./gto_fastq_minimum_local_quality_score_reverse -h

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

Input parameters

The gto_fastq_minimum_local_quality_score_reverse 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_reverse [options] [[--] args]
or: ./gto_fastq_minimum_local_quality_score_reverse [options]

It filters the reverse 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_reverse -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
GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACCAAGTTACCCTTAACAACTTAAGGGTTTTCAAATAGA
+SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9ICIIIIIIIIIIIIIIIIIIIIDIIIIIII>IIIIII/
@SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72
GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGAAGCAGAAGTCGATGATAATACGCGTCGTTTTATCAT
+SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBIIIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I

Output

The output of the gto_fastq_minimum_local_quality_score_reverse 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
GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACCAAGTTACCCTTAACAACTTAAGGGTTTTCAAATAGA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9ICIIIIIIIIIIIIIIIIIIIIDIIIIIII>IIIIII/
Total reads    : 2
Trimmed reads  : 1