How to run cutadapt in parallel

Question

[Javad]

Hi everybody,

I am using cutadapt to trim and QC of my NGS data but it is damn slow. I have also installed GNU Parallel to run it in parallel but I couldn't. To be honest, the tutorial of GNU Parallel is so complicated and I couldn't figure out how to run cutadapt in parallel with it. let's assume that I have the following cutadapt command and I want to run it using GNU Parallel.

cutadapt -u 15 -o output.fastq input.fastq

how would you run it in parallel using GNU Parallel?

Thanks in advance

[cschu181]

cutadapt 1.5 supports multi core now. http://cutadapt.readthedocs.io/en/stable/guide.html (search for "core").

[Pierre Lindenbaum]

To be honest, the tutorial of GNU Parallel is so complicated

to be honest, it's not IMHO.

What have you tried so far ? Show us the command lines please.

[Javad]

I ran this one for example:

parallel -k -j 24 cutadapt -u 15 -o output.fastq input.fastq

What can I change to make it right? Thanks a lot...

[Pierre Lindenbaum]

moving you to the way:

echo -e "input1.fastq\ninput2.fastq" |\
parallel  echo '{}' '{.}'.cutadapt.fastq