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.
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
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
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
GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACCAAGTTACCCTTAACAACTTAAGGGTTTTCAAATAGA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9ICIIIIIIIIIIIIIIIIIIIIDIIIIIII>IIIIII/
@SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72
GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGAAGCAGAAGTCGATGATAATACGCGTCGTTT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBIIIIIIIIIIIIIIIIIIIIIIIGII>IIII
Total reads : 2
Trimmed reads : 1