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.
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
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