cryptsetup -y -c twofish-cbc-essiv:sha256 luksFormat /dev/mapper/memelabs--de2-misc
cryptsetup luksOpen /dev/mapper/memelabs--de2-misc misc-crypt
mkfs.ext3 -b 4096 -E stride=8 /dev/mapper/misc-crypt
echo "misc-crypt /dev/mapper/memelabs--de2-misc none luks,check=ext2,retry=1" >> /etc/crypttab
echo "/dev/mapper/misc-crypt /misc-crypt ext3 defaults 1 2" >> /etc/fstab
mkdir /misc-crypt
update-initramfs -u -k all

For using latter:

cryptsetup luksOpen /dev/mapper/memelabs--de2-misc misc-crypt
mount /dev/mapper/misc-crypt /misc-crypto
umount /misc-crypt
cryptsetup luksClose misc-crypt

For encrypted swap look in the documentation of crytosetup of debian.