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FelixKrueger / TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
GNU General Public License v3.0
459 stars 149 forks source link

Optionally use igzip for decompression of gzipped files. #149

Closed ghuls closed 1 year ago

ghuls commented 1 year ago

igzip (https://github.com/intel/isa-l/) is quite a bit faster than standard gzip/pigz for decompressing gzipped files.

Total runtime might not be that much faster with igzip as in most cases igzip will only consume around 20% CPU as other commands in the pipeline can't keep up. But it lowers the total amount of CPU used by TrimGalore.

cutadapt also uses python-isal/igzip under the hood via xopen to read FASTQ files.

FelixKrueger commented 1 year ago

Thanks for your contribution, I hope it'll help to make a small difference.