Edgenl2g

Introduction

Essentials of Edinburgh Genomics' Linux for Genomics course

Duration

• 1 day
• 2/3's core linux 1/3 genomics focus

Contents

Core Linux

• The shell and commands
• Getting help
• Files and directories
• Navigating the file system
• File management*
• Permissions
• Accessing files
• Downloading remote files
• Zipping and unzipping files
• Pipes and redirects
• Filtering / manipulating file content
• Shell scripts
• Process management

Focused Genomics

Command-line tools for genomics

• seqtk
• bioawk
• samtools
• bedtools
• tabix