The bioBakery help forum

Feature request for kneaddata: add option to compress output fastq files

I cannot find the option in kneaddata to compress the output fastq files. When running kneaddata in parallel, the output uncompressed fastq files can take up >1T disk space in a day.
Could you add an option to kneaddata to compress the output fastq files?

Hi @dwuab ,

Thank you for reaching out to the biobakery lab. We are currently working on getting the option added to Kneaddata and will let you know soon when released.

Regards,
Sagun