GNU Parallel, FTW!

If you have access to a HPC cluster, open a interactive job session. In my case I have a 64 core node, so I do it as:

qsub -I -l nodes=1:ppn=64 -l walltime=1:00:00

then run gunzip on all 64 processors

parallel -j64 "gunzip {}" ::: *.fastq.gz

I'll be done in no time!

$ gunzip *.gz

or

$ for f in *.gz; do gunzip $f; done

Or don't.

pass them compressed if the tool handles it ,or decompress on the fly i.e.

zcat file.gz | whatever_tool

There are a bunch of utilities for processing gzip without explicitly writing out the unzipped file

http://www.nongnu.org/zutils/manual/zutils_manual.html

Hi,

PIGZ could be potential solution, its parallel version of GZip and uses the multi threading out of the box with so many other parameters to tweak the performance. You can find one here: http://zlib.net/pigz/

You can simply run pigz -d *.gz to extract the .gz files

Thanks

http://stackoverflow.com/questions/16038087/extract-all-gz-in-a-directory-linux

It might do the job

gunzip '*.gz'

gunzip *.fastq.gz will do the job!