README.md

A UNIX/programming/bioinformatics cheatsheet. Based on Tom's original idea of a repository of useful tips for Merlin use here, but with more personal stuff in it.

Bash

General

• Split strings in Bash
• Aliases
• Helpful functions
• stdout & stderr
• for, while, if
• Installing/searching for packages/dependencies
• Path
• Arithmetic expansion
• Finding files/directories
• Zipping/unzipping files/directories

Parallelisation and Priority

• Nice and Re-Nice
• nohup
• GNU parallel - intro
• killing processes

Awk

• awk cheat sheet

Terminal editors

• nano commands

Misc

• Command Prompt Appearance

R

• commandArgs
• checksum_check.R

Python

• Python basics, including parsing arguments on the command line

Bioinformatics

Fasta files

• useful shell operations on fasta files

BAM files

• useful shell operations on BAM files

VCF files

• useful shell operations on VCF files

Git/github

• Basic use
• Making websites on Github