Command Line Tools for Genomic Data Science (Coursera)

Command Line Tools for Genomic Data Science (Coursera)

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.

Class Deals by MOOC List - Click here and see Coursera's Active Discounts, Deals, and Promo Codes.

Course of the 5 of 8 of the Genomic Data Science Specialization.

Syllabus

WEEK 1
In this module, you will be introduced to command Line Tools for Genomic Data Science

WEEK 2
In this module, we'll be taking a look at Sequences and Genomic Features in a sequence of 10 presentations.

WEEK 3
In this module, we'll be going over Alignment and Sequence Variation in another sequence of 8 presentations.

WEEK 4
In this module, we'll be going over Tools for Transcriptomics in a sequence of 6 presentations.

Go to Class
MOOC List is learner-supported. When you buy through links on our site, we may earn an affiliate commission.

Related Courses

Plant Bioinformatics (Coursera) Coursera
University of Toronto

Plant Bioinformatics (Coursera)

The past 15 years have been exciting ones in plant biology. Hundreds of plant genomes have been sequenced, RNA-seq has enabled transcriptome-wide expression profiling, and a proliferation of "-seq"-based methods has permitted protein-protein and protein-DNA interactions to be determined cheaply and in a high-throughput manner. These data sets in turn allow us to generate hypotheses at the click of a mouse.

Jun 1st 2026
5-12 Weeks
Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen (Coursera) Coursera
University of California, San Diego

Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen (Coursera)

In this course, you will follow in the footsteps of the bioinformaticians investigating the COVID-19 outbreak by assembling the SARS-CoV-2 genome. Whether you’re new to the world of computational biology, or you’re a bioinformatics expert seeking to learn about its applications in the COVID-19 pandemic, or somewhere in between, this course is for you!

Jun 1st 2026
2 Weeks
Introduction to Genomic Technologies (Coursera) Coursera
Johns Hopkins University

Introduction to Genomic Technologies (Coursera)

This course introduces you to the basic biology of modern genomics and the experimental tools that we use to measure it. We'll introduce the Central Dogma of Molecular Biology and cover how next-generation sequencing can be used to measure DNA, RNA, and epigenetic patterns. You'll also get an introduction to the key concepts in computing and data science that you'll need to understand how data from next-generation sequencing experiments are generated and analyzed.

Jun 22nd 2026
4 Weeks
Hacking COVID-19 — Course 2: Decoding SARS-CoV-2's Secrets (Coursera) Coursera
University of California, San Diego

Hacking COVID-19 — Course 2: Decoding SARS-CoV-2's Secrets (Coursera)

In this course, you will follow in the footsteps of the bioinformaticians investigating the COVID-19 outbreak by annotating the SARS-CoV-2 genome and using the annotation to design a COVID-19 diagnostic test. Whether you’re new to the world of computational biology, or you’re a bioinformatics expert seeking to learn about its applications in the COVID-19 pandemic, or somewhere in between, this course is for you!

Jun 1st 2026
2 Weeks
The Unix Workbench (Coursera) Coursera
Johns Hopkins University

The Unix Workbench (Coursera)

Unix forms a foundation that is often very helpful for accomplishing other goals you might have for you and your computer, whether that goal is running a business, writing a book, curing disease, or creating the next great app. The means to these goals are sometimes carried out by writing software. Software can’t be mined out of the ground, nor can software seeds be planted in spring to harvest by autumn. Software isn’t produced in factories on an assembly line. Software is a hand-made, often bespoke good. If a software developer is an artisan, then Unix is their workbench.

Jun 8th 2026
4 Weeks
Python and Rust with Linux Command Line Tools (Coursera) Coursera
Duke University

Python and Rust with Linux Command Line Tools (Coursera)

This course is designed for beginners and those with some programming experience in either Python or Rust that want to implement automation and utilities in the command-line. Although no prior knowledge of Python or Rust is required, basic programming knowledge is recommended as well as some familiarity with the command-line interface (CLI).

Jun 15th 2026
4 Weeks
Linux Basics: The Command Line Interface - 6 (Coursera) Coursera
Institut Mines-Telecom,Dartmouth College

Linux Basics: The Command Line Interface - 6 (Coursera)

This course will introduce you to Linux, a powerful operating system used by most professional developers! Why add Linux to your C programming skills? Most people use Linux without knowing it! Whether you use a smartphone, search the web, or use an ATM, each time Linux is involved somewhere in the background. It is the most used operating system for embedded devices and high-performance servers. It is also the most common operating system used by developers to create software applications.

Jun 22nd 2026
3 Weeks
Finding Hidden Messages in DNA (Bioinformatics I) (Coursera) Coursera
University of California, San Diego

Finding Hidden Messages in DNA (Bioinformatics I) (Coursera)

This course begins a series of classes illustrating the power of computing in modern biology. Please join us on the frontier of bioinformatics to look for hidden messages in DNA without ever needing to put on a lab coat. In the first half of the course, we investigate DNA replication, and ask the question, where in the genome does DNA replication begin? We will see that we can answer this question for many bacteria using only some straightforward algorithms to look for hidden messages in the genome.

Jun 22nd 2026
5-12 Weeks
Big Data Science with the BD2K-LINCS Data Coordination and Integration Center (Coursera) Coursera
Icahn School of Medicine at Mount Sinai

Big Data Science with the BD2K-LINCS Data Coordination and Integration Center (Coursera)

In this course we briefly introduce the DCIC and the various Centers that collect data for LINCS. We then cover metadata and how metadata is linked to ontologies. We then present data processing and normalization methods to clean and harmonize LINCS data. This follow discussions about how data is served as RESTful APIs. Most importantly, the course covers computational methods including: data clustering, gene-set enrichment analysis, interactive data visualization, and supervised learning. Finally, we introduce crowdsourcing/citizen-science projects where students can work together in teams to extract expression signatures from public databases and then query such collections of signatures against LINCS data for predicting small molecules as potential therapeutics.

Jun 1st 2026
5-12 Weeks
Finding Mutations in DNA and Proteins (Bioinformatics VI) (Coursera) Coursera
University of California, San Diego

Finding Mutations in DNA and Proteins (Bioinformatics VI) (Coursera)

In previous courses in the Specialization, we have discussed how to sequence and compare genomes. This course will cover advanced topics in finding mutations lurking within DNA and proteins. In the first half of the course, we would like to ask how an individual's genome differs from the "reference genome" of the species.

Jun 22nd 2026
5-12 Weeks