How to convert FASTQ format to FASTA on the local computer (without Internet) under Windows operation system? Is it necessary to use another operating system?
Hi Andrii
Try the program on this website: http://www.blaststation.com/freestuff/en/fastq2fasta.php#win You might have to download it to a USB stick on another computer and then transfer to the primary computer.
Alternatively, you could install a programming language like perl (perl.org) or a command line linux tool like Cygwin (http://www.cygwin.com/) and use one of the many scripts out there (do a google search for "fastq to fasta".
Best of luck!
If you have Python installed on your machine with BioPython libraries, you can run a one-liner:
$PYTHON -c "from Bio import SeqIO;SeqIO.convert('$s.fq','fastq','$s.fasta','fasta')"
where $PYTHON is your Python instance and $s is the stub of your file name.
From a Windows CMD shell (just type cmd in the "search programs and files" area), and type or paste the command.
Python for windows can be downloaded here: http://www.python.org/download/releases/2.7.3/
Biopython here: http://biopython.org/DIST/biopython-1.60.win32-py2.7.exe
Just install them in that order.
You may need to adjust your PATH environment variable by adding C:\Python27; to the front of it..
What Hai Fang wrote is a good solution; however, it should be:
zcat input_file.fastaq.gz | paste - - - - | awk '{print ">"$1"\n"$3}' > output_file.fa
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