Optionally use igzip for decompression of gzipped files. #149
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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.
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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.