Block 3: Basic Linux

Most of the bioinformatic tools are programs designed to be used through a console, generally in an Unix system, such as NGS mapping tools (bwa or bowtie…), sequence assembly tools (mira, velvet, abyss…). It is essential the knowledge of basic linux commands to execute these programs, control the resources usage of the machine or preprocess some the results. Additionally there are some “basic recipes” to manipulate big files, such as “grep -c ‘>’ fastafile” to count the number of sequences in fasta file.

This session will be divided into two days: March 12th and March 19th.

  • The presentation for the 12th (Part 1) can be found: Block3_BasicLinux-Lecture_part1
  • The exercises: Block3_BasicLinux-Exercises_part1
  • The solutions: Block3_BasicLinux-Solutions_part1
  • The presentation for the 19th (Part 2) can be found:BasicLinux
  • The exercises: Block3_BasicLinux_part2-Exercises
  • The solutions: Block3_BasicLinux_part2-Solutions
  • An small summary of the Linux commands: LinuxCommandsSummary

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