Genomics Workshop: Glossary

Key Points

Shell Basics
  • Use cd, pwd and ls to navigate the file system and inspect its contents

  • Use cp, mv and rm to copy, move and remove files or directories

  • Use mkdir and touch to create new empty directories and files respectively

  • The location of a file or folder, i.e., the path to the file or folder can be relative or absolute. An absolute path always starts from the root directory (/)

  • Text files can be created and edited from the command-line using an editor like nano or vim

Running programs using the shell
  • All files and folders have an owner (a user) and a group (a collection of users) associated with them

  • Files and folders can have read (r), write (w) and execute (x) permissions for the file owner, members of the group associated with the file, and for all users

  • Executable files can be run by providing the path to the file on the command line

  • The output of a command can be redirected to a file using >, or to another program using |

  • You can sort text using the sort command

Interacting with the Palmetto Cluster
More about the command-line
  • Keypoint 1

  • Keypoint 2

More about Palmetto Cluster
  • Keypoint 1

  • Keypoint 2

Navigating the NCBI database
Variant calling workflow
Parallel Variant Calling Workflow


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