Summary and Schedule

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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.

Please note that workshop materials for working with Genomics data in R are in “alpha” development. These lessons are available for review and for informal teaching experiences, but are not yet part of The Carpentries’ official lesson offerings.

Interested in teaching these materials? We have an onboarding video and accompanying slides available to prepare Instructors to teach these lessons. After watching this video, please contact team@carpentries.org so that we can record your status as an onboarded Instructor. Instructors who have completed onboarding will be given priority status for teaching at centrally-organized Data Carpentry Genomics workshops.

Frequently Asked Questions

Read our FAQ to learn more about Data Carpentry’s Genomics workshop, as an Instructor or a workshop host.

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.

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.

Common Schedules

Schedule A (2 days OR 4 half days)

Schedule B (2 days OR 4 half days)

Schedule C (3 days OR 6 half days)

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.

Overview

This workshop is designed to be run on pre-imaged Amazon Web Services (AWS) instances. All of the data and most of the software used in the workshop are hosted on an Amazon Machine Image (AMI). Some additional software, detailed below, must be installed on your computer.

Please follow the instructions below to prepare your computer for the workshop:

  • Required additional software + Option A OR
  • Required additional software + Option B

Required additional software

This lesson requires a working spreadsheet program. If you don’t have a spreadsheet program already, you can use LibreOffice. It’s a free, open source spreadsheet program. Directions to install are included for each Windows, Mac OS X, and Linux systems below. For Windows, you will also need to install either Git Bash, PuTTY, or the Ubuntu Subsystem.

  • Visit the LibreOffice installation page. The version for Windows should automatically be selected. Click Download Version X.X.X (whichever is the most recent version). You will go to a page that asks about a donation, but you don’t need to make one. Your download should begin automatically.
  • Once the installer is downloaded, double click on it and LibreOffice should install.
  • Download the Git for Windows installer. Run the installer and follow the steps below:
    • Click on “Next” four times (two times if you’ve previously installed Git). You don’t need to change anything in the Information, location, components, and start menu screens.
    • From the dropdown menu select “Use the Nano editor by default” (NOTE: you will need to scroll up to find it) and click on “Next”.
    • On the page that says “Adjusting the name of the initial branch in new repositories”, ensure that “Let Git decide” is selected. This will ensure the highest level of compatibility for our lessons.
    • Ensure that “Git from the command line and also from 3rd-party software” is selected and click on “Next”. (If you don’t do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the “Git from the command line and also from 3rd-party software” option.)
    • Ensure that “Use the native Windows Secure Channel Library” is selected and click on “Next”.
    • Ensure that “Checkout Windows-style, commit Unix-style line endings” is selected and click on “Next”.
    • Ensure that “Use Windows’ default console window” is selected and click on “Next”.
    • Ensure that “Default (fast-forward or merge) is selected and click”Next”
    • Ensure that “Git Credential Manager Core” is selected and click on “Next”.
    • Ensure that “Enable file system caching” is selected and click on “Next”.
    • Click on “Install”.
    • Click on “Finish”.
    • Check the settings for you your “HOME” environment variable.
      • If your “HOME” environment variable is not set (or you don’t know what this is):
      • Open command prompt (Open Start Menu then type cmd and press [Enter])
      • Type the following line into the command prompt window exactly as shown: setx HOME "%USERPROFILE%"
      • Press [Enter], you should see SUCCESS: Specified value was saved.
      • Quit command prompt by typing exit then pressing [Enter]
  • An alternative option is to install PuTTY. For most newer computers, click on putty-64bit-X.XX-installer.msi to download the 64-bit version. If you have an older laptop, you may need to get the 32-bit version putty-X.XX-installer.msi. If you aren’t sure whether you need the 64 or 32 bit version, you can check your laptop version. Once the installer is downloaded, double click on it, and PuTTY should install.
  • Another alternative option is to use the Ubuntu Subsystem for Windows. This option is only available for Windows 10 - the Microsoft documentation provides detailed instructions for installing Windows 10.
  • Visit the LibreOffice installation page. The version for Mac should automatically be selected. Click Download Version X.X.X (whichever is the most recent version). You will go to a page that asks about a donation, but you don’t need to make one. Your download should begin automatically.
  • Once the installer is downloaded, double click on it and LibreOffice should install.
  • Visit the LibreOffice installation page. The version for Linux should automatically be selected. Click Download Version X.X.X (whichever is the most recent version). You will go to a page that asks about a donation, but you don’t need to make one. Your download should begin automatically.
  • Once the installer is downloaded, double click on it and LibreOffice should install.

If you are signed up to take a Genomics Data Carpentry workshop, you do not need to worry about setting up an AMI instance. The Carpentries staff will create an instance for you and this will be provided to you at no cost. This is true for both self-organized and centrally-organized workshops. Your Instructor will provide instructions for connecting to the AMI instance at the workshop.

If you would like to work through these lessons independently, outside of a workshop, you will need to start your own AMI instance. Follow these instructions on creating an Amazon instance. Use the AMI ami-04dd77cd58b3ec654 (Data Carpentry Genomics with R 4.2) listed on the Community AMIs page. Please note that you must set your location as N. Virginia in order to access this community AMI. You can change your location in the upper right corner of the main AWS menu bar. The cost of using this AMI for a few days, with the t2.medium instance type is very low (about USD $1.50 per user, per day). Data Carpentry has no control over AWS pricing structure and provides this cost estimate with no guarantees. Please read AWS documentation on pricing for up-to-date information.

If you’re an Instructor or Maintainer or want to contribute to these lessons, please get in touch with us and we will start instances for you.

Option B: Using the lessons on your local machine

While not recommended, it is possible to work through the lessons on your local machine (i.e. without using AWS). To do this, you will need to install all of the software used in the workshop and obtain a copy of the dataset. Instructions for doing this are listed below.

Data

The data used in this workshop is available on FigShare. Because this workshop works with real data, be aware that file sizes for the data are large. Please read the FigShare page for information about the data and access to the data files.

More information about these data will be presented in the first lesson of the workshop.

Software

Software Version Manual Available for Description
FastQC 0.11.9 Link Linux, MacOS, Windows Quality control tool for high throughput sequence data.
Trimmomatic 0.39 Link Linux, MacOS, Windows A flexible read trimming tool for Illumina NGS data.
BWA 0.7.17 Link Linux, MacOS Mapping DNA sequences against reference genome.
SAMtools 1.9 Link Linux, MacOS Utilities for manipulating alignments in the SAM format.
BCFtools 1.9 Link Linux, MacOS Utilities for variant calling and manipulating VCFs and BCFs.
IGV Link Link Linux, MacOS, Windows Visualization and interactive exploration of large genomics datasets.

QuickStart Software Installation Instructions

These are the QuickStart installation instructions. They assume familiarity with the command line and with installation in general. As there are different operating systems and many different versions of operating systems and environments, these may not work on your computer. If an installation doesn’t work for you, please refer to the user guide for the tool, listed in the table above.

We have installed software using Conda. Conda is a package manager that simplifies the installation process. Please first install Conda through the Miniconda installer (see below) before proceeding to the installation of individual tools. For more information on Miniconda, please refer to the Conda documentation.

Conda

To install Conda, type:

BASH 

$ curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash Miniconda3-latest-Linux-x86_64.sh

Then, follow the instructions that you are prompted with on the screen to install Conda.

To install Conda, type:

BASH 

$ curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
$ bash Miniconda3-latest-MacOSX-x86_64.sh

Then, follow the instructions that you are prompted with on the screen to install Conda.

FastQC

To install FastQC, type:

BASH 

$ conda install -c bioconda fastqc=0.11.9

If you prefer to install from source, follow the directions below:

BASH 

$ cd ~/src
$ curl -O http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip
$ unzip fastqc_v0.11.9.zip

Link the fastqc executable to the ~/bin folder that you have already added to the path.

BASH 

$ ln -sf ~/src/FastQC/fastqc ~/bin/fastqc

Due to what seems a packaging error the executable flag on the fastqc program is not set. We need to set it ourselves.

BASH 

$ chmod +x ~/bin/fastqc

Test your installation by running:

BASH 

$ fastqc -h

Trimmomatic

BASH 

conda install -c bioconda trimmomatic=0.39

If you prefer to install from source, follow the directions below:

BASH 

$ cd ~/src
$ curl -O http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip
$ unzip Trimmomatic-0.39.zip

The program can be invoked via:

$ java -jar ~/src/Trimmomatic-0.39/trimmomatic-0.39.jar

The ~/src/Trimmomatic-0.39/adapters/ directory contains Illumina specific adapter sequences.

BASH 

$ ls ~/src/Trimmomatic-0.39/adapters/

Test your installation by running: (assuming things are installed in ~/src)

BASH 

$ java -jar ~/src/Trimmomatic-0.39/trimmomatic-0.39.jar

To simplify the invocation you could also create a script in the ~/bin folder:

BASH 

$ echo '#!/bin/bash' > ~/bin/trimmomatic
$ echo 'java -jar ~/src/Trimmomatic-0.39/trimmomatic-0.39.jar $@' >> ~/bin/trimmomatic
$ chmod +x ~/bin/trimmomatic

Test your script by running:

BASH 

$ trimmomatic

BWA

BASH 

conda install -c bioconda bwa=0.7.17=ha92aebf_3

If you prefer to install from source, follow the instructions below:

BASH 

$ cd ~/src
$ curl -OL http://sourceforge.net/projects/bio-bwa/files/bwa-0.7.17.tar.bz2
$ tar jxvf bwa-0.7.17.tar.bz2
$ cd bwa-0.7.17
$ make
$ export PATH=~/src/bwa-0.7.17:$PATH

Test your installation by running:

BASH 

$ bwa

SAMtools

BASH 

$ conda install -c bioconda samtools=1.9=h8ee4bcc_1

SAMtools Versions

SAMtools has changed the command line invocation (for the better). But this means that most of the tutorials on the web indicate an older and obsolete usage.

Using SAMtools version 1.9 is important to work with the commands we present in these lessons.

If you prefer to install from source, follow the instructions below:

BASH 

$ cd ~/src
$ curl -OkL https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
$ tar jxvf samtools-1.9.tar.bz2
$ cd samtools-1.9
$ make

Add directory to the path if necessary:

BASH 

$ echo export `PATH=~/src/samtools-1.9:$PATH` >> ~/.bashrc
$ source ~/.bashrc

Test your installation by running:

BASH 

$ samtools

BCFtools

BASH 

$ conda install -c bioconda bcftools=1.9

If you prefer to install from source, follow the instructions below:

BASH 

$ cd ~/src
$ curl -OkL https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2
$ tar jxvf bcftools-1.9.tar.bz2
$ cd bcftools-1.9
$ make

Add directory to the path if necessary:

BASH 

$ echo export `PATH=~/src/bcftools-1.9:$PATH` >> ~/.bashrc
$ source ~/.bashrc

Test your installation by running:

BASH 

$ bcftools

IGV