SC2 Sequencing Cheats

File manipulation/bioinformatics-type scripts that my colleuges have found useful in sequencing SARS-CoV2 (SC2).

These scripts have various purposes, uses, and instructions. The only unifying thing about them is that they were all written for SC2 and related sequencing. Please check the README file in each directory for more detailed instructions.

Encryption

NOTICE: Some files in this repository are encrypted using git-crypt. git-crypt works on a repository-wide basis, meaning that decryption must occur on the entire repository.

Installing git-crypt

Ubuntu, Debian, etc.

sudo apt-get install git-crypt -y

Fedora, CentOS, RHEL, etc.

sudo yum install git-crypt -y

MacOS

Install Homebrew first. Then

brew install git-crypt

Windows

There are no official git-crypt builds for Windows. I repeat, git-crypt does not exist for Windows regardless of what others may tell you. If possible, you may use the Windows Subsystem for Linux, but you cannot use native git-crypt.

Decrypting the repository

Encryption is GPG-based. If your GPG key has been added to the repository (you know if you have access), then run

git clone https://github.com/MillironX/sc2-sequencing.git && cd sc2-sequencing
git-crypt unlock

The files will now be decrypted and can be usable.

If you need to copy your GPG keys to a new machine to be able to decrypt the files, follow the instructions at https://www.phildev.net/pgp/gpg_moving_keys.html under "Copy Just Your Keys."