Command Line Tools for Genomic Data Science

Introduces to the commands that you need to manage and analyze directories, files, and large sets of genomic data. This is the fourth course in the Genomic Big Data Science Specialization from Johns Hopkins University.

About The Course

This class will cover an introduction to command line tools for managing genomic data. It will start with basic Unix commands for managing files and directories, followed by a review of the main starndardized data formats and hands-on instruction on how to use popular tools such as Samtools, Bedtools, Bowtie, and application specific technologies such as Bcftools and Cufflinks.

Frequently Asked Questions

  • Do I need any special materials or supplies to take this course? 
A computer with a Unix command-line interface, this includes computers running Linux, Apple OS X, or Windows computers with extra software installed. If you don’t have  computer running a Unix command-line interface, you may optionally only take the Galaxy course and still complete the Specialization.
  • Do I have to take this course before taking other courses in the Genomic Big Data Science Specialization?
You are strongly encouraged to take this course fourth in the sequence.

Recommended Background

Prerequisite: Introduction to Sequencing Technologies

The target audience of this course are individuals in the molecular or computational sciences who want how to learn how to perform basic computational biology. This class is “hands on” and designed to get you started with the tools you need to perform Genomic Data Science.