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I am trying to create a custom Ubuntu based distro but I can't figure out how to create compressed iso file system.

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You use squashfs

The instructions are on the wiki pages :

https://help.ubuntu.com/community/LiveCDCustomization#Assembling_the_file_system

https://help.ubuntu.com/community/LiveCDCustomizationFromScratch#Compress_the_chroot

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