General Information

Data Carpentry’s aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain. This workshop teaches data management and analysis for genomics research including: best practices for organization of bioinformatics projects and data, use of command-line utilities, use of command-line tools to analyze sequence quality and perform variant calling, and connecting to and using cloud computing. This workshop is designed to be taught over two full days of instruction.

Registration: Please complete the online registration form at https://forms.gle/EmrC8S5e3ERuDKZV7. Limited space is available. The workshop is free to attend but a R500 no-show fee will be payable by a registered participant who does not show up to the workshop without giving the workshop organisers at least 3 days notice.

The workshop is part of a series of Digital Literacy workshops supported by the Big Data and Informatics Research Flagship and funded through the University Capacity Development Programme (UCDP) at UKZN.

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They are also required to abide by Data Carpentry's Code of Conduct.

Contact: Please email tadigutsah@gmail.com, oluwafisayo.kaka@gmail.com for more information.

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Getting Started

This lesson assumes that learners have no prior experience with the tools covered in the workshop. However, learners are expected to have some familiarity with biological concepts, including the concept of genomic variation within a population. Participants should bring their own laptops and plan to participate actively.

To get started, follow the directions in the Setup tab to get access to the required software and data for this workshop.

Data

This workshop uses data from a long term evolution experiment published in 2016: Tempo and mode of genome evolution in a 50,000-generation experiment by Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL, Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D, and Lenski RE. (doi: 10.1038/nature18959)

All of the data used in this workshop can be downloaded from Figshare. More information about this data is available on the Data page.

Workshop Overview

Lesson	Overview
Project organization and management	Learn how to structure your metadata, organize and document your genomics data and bioinformatics workflow, and access data on the NCBI sequence read archive (SRA) database.
Introduction to the command line	Learn to navigate your file system, create, copy, move, and remove files and directories, and automate repetitive tasks using scripts and wildcards.
Data wrangling and processing	Use command-line tools to perform quality control, align reads to a reference genome, and identify and visualize between-sample variation.
Introduction to cloud computing for genomics	Learn how to work with Amazon AWS cloud computing and how to transfer data between your local computer and cloud resources.

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.

Optional Additional Lessons

Lesson	Overview
Intro to R and RStudio for Genomics	Use R to analyze and visualize between-sample variation.

Teaching Platform

This workshop is designed to be run on pre-imaged Amazon Web Services (AWS) instances. All the software and data used in the workshop are hosted on an Amazon Machine Image (AMI). If you want to run your own instance of the server used for this workshop, follow the directions in the Setup tab.