Program gto_amino_acid_from_fastq

The gto_amino_acid_from_fastq converts DNA sequences in the FASTQ file format to an amino acid sequence.

For help type:

./gto_amino_acid_from_fastq -h

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

Input parameters

The gto_amino_acid_from_fastq 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: ../../bin/gto_amino_acid_from_fastq [options] [[--] args]
or: ../../bin/gto_amino_acid_from_fastq [options]

It converts FASTQ file format to an amino acid sequence (translation).

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

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

-f, --frame= Translation codon frame (1, 2 or 3)

Example: ../../bin/gto_amino_acid_from_fastq < input.fastq > output.prot

An example of such an input file is:

@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72
+SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72
@SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72
+SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72


The output of the gto_amino_acid_from_fastq program is an amino acid sequence.

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