Edgenl2g

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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
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