Program gto_fastq_reverse

The gto_fastq_reverse reverses the ACGT bases order for each read in a FASTQ file format.

For help type:

./gto_fastq_reverse -h


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

Input parameters

The gto_fastq_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_reverse [options] [[--] args]
or: ./gto_fastq_reverse [options]

It reverses the ACGT bases order for each read in a FASTQ file.

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

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

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


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_reverse program is the FASTQ file complement with the flag ''(Reversed)'' added in the header.

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

@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72 (Reversed)
AGATAAACTTTTGGGAATTCAACAATTCCCATTGAACCACCCTAAACTGCGGTAGCCGTCGCCGGTAGTGGG
+
/IIIIII>IIIIIIIDIIIIIIIIIIIIIIIIIIIICI9GI9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72 (Reversed)
TACTATTTTGCTGCGCATAATAGTAGCTGAAGACGAAGTCTAAGAATTTTATGTTTGCAGCATAGGGACTTG
+
I8)I-IIIII>IIGIIIIIIIIIIIIIIIIIIIIIIIBI6IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII