Program gto_fastq_unpack

The gto_fastq_unpack unpacks the FASTQ reads packaged using the gto_fastq_pack tool.

For help type:

./gto_fastq_unpack -h


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

Input parameters

The gto_fastq_unpack program needs two streams for the computation, namely the input and output standard. The input stream is a packaged FASTQ file.

The attribution is given according to:

Usage: ./gto_fastq_unpack [options] [[--] args]
or: ./gto_fastq_unpack [options]

It unpacks the FASTQ reads packaged using the gto_fastq_pack tool.

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

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

Optional
-s, --scores When active, the application show the scores first

Example: ./gto_fastq_unpack -s < input.fastqpack > output.fastq


An example of such an input file is:

GNNTGATGGCCGCTGCCGATGGCGNANAATCCCACCAANATACCCTTAACAACTTAAGGGTTNTCAAATAGA
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9ICIIIIIIIIIIIIIIIIIIIIDIIIIIII>IIIIII/
SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72+ 0
NTTCAGGGATACGACGNTTGTATTTTAAGAATCTGNAGCAGAAGTCGATGATAATACGCGNCGTTTTATCAN
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBIIIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I
SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72+ 1


Output

The output of the gto_fastq_unpack program is a FASTQ file.

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
GNNTGATGGCCGCTGCCGATGGCGNANAATCCCACCAANATACCCTTAACAACTTAAGGGTTNTCAAATAGA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9ICIIIIIIIIIIIIIIIIIIIIDIIIIIII>IIIIII/
@SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72
NTTCAGGGATACGACGNTTGTATTTTAAGAATCTGNAGCAGAAGTCGATGATAATACGCGNCGTTTTATCAN
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBIIIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I