Introduction to Reproducible Genomics: Data Carpentry

May 13-14, 2019

9:00 am - 5:00 pm

Instructors: Mateusz Kuzak, Toby Hodges

Helpers: Christof De Bo

General Information

This is a Data Carpentry Workshop, with a special focus on sequence handling for variant calling using the cloud resources, the workshop will introduce you to Genomic concepts and scripting. For those unfamiliar with the concept, Data Carpentry aims at systematically delivering workshops on the fundamental data skills needed to conduct research. What you will learn during the workshop will largely influence the way in which you handle data in a fully independent way, free from proprietary software and storage platforms. The workshop will be run by Mateusz Kuzak from the Dutch Techcentre for Life Sciences and Toby Hodges from EMBL BioIT, both highly qualified instructors of the Carpentries carpentries.org. The contents of this workshop will be the Genomics Curriculum. Check what to expect if you’re attending a workshop. For more details about what will be covered please see the schedule below. Attendance will be granted for FREE to up to 35 participants that need to apply before April 30th at noon.

Who: The course is aimed at graduate students and other researchers who are interested in learning how bioinformatics is done in automated way using a server infrastructure. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

What: We will start with an introduction to the command line and use of command line utilities to analyze sequence quality and perform variant calling. All using publicly available datasets and connecting to and using cloud computing.

Where: Overwale 3, 9000 Gent. Clemenspoort: Zaal Neumann. Get directions with OpenStreetMap or Google Maps.

When: May 13-14, 2019. Add to your Google Calendar.

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 should have a few specific software packages installed (listed below). They are also required to abide by Data Carpentry's Code of Conduct.

Digital materials can be found linked to the schedule. If we can help making learning easier for you please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email bits@vib.be for more information.

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Schedule

Day 1 - May 13th

Before starting Make sure you have filled in the Pre-workshop survey
Morning Project organization for genomics
MorningCloud Genomics
AfternoonShell for genomics
Evening END

Day 2 - May 14th

Morning Data wrangling and processing
Afternoon Data wrangling and processing continuation
Evening Make sure you have filled in the Post-workshop survey
END

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

Syllabus

Project Organization

  • Data Tidiness
  • Planning for NGS Projects
  • Examining Data on the NCBI SRA Database
  • Reference

Introduction to Cloud Computing for Genomics

  • Why of cloud computing
  • Logging onto Cloud
  • Basic functions
  • Advanced Functions
  • Reference

Introduction to the Command Line for Genomics

  • Navigating Files and Directories
  • Redirection
  • Writing Shell Scripts
  • Reference

Data Wrangling and Processing for Genomics

  • Assessing Read Quality (FASTQ)
  • Trimming and Filtering
  • Variant Calling Workflow
  • Automating a Variant Calling Workflow
  • Reference

Setup

To participate in a Data Carpentry workshop, you will need working copies of the software described below. Please make sure to install everything and try opening it to make sure it works before the start of your workshop. If you run into any problems, please feel free to email the instructor or arrive early to your workshop on the first day. Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.

Platform-specific Notes

This workshop will be using the software outlined in the install instructions below. Please see the section for your operating system for those directions.

Windows

Please go through all the installation steps below and make sure that you not only installed them, but start them up to make sure they're working. If you have any problems, don't hesitate to email the instructors to ask for help, or arrive early on the first day of the workshop to get help.

  1. A spreadsheet program

    2. For this workshop you will need a spreadsheet program. Many people already have Microsoft Excel installed, and if you do, you're set!
    If you need a spreadsheet program, there are a few other options, like OpenOffice and LibreOffice. Install instructions for LibreOffice, which is free and open source, are here.
    • Download the Installer
      Install LibreOffice by going to the installation page. The version for Windows should automatically be selected. Click Download Version 6.0.3 or later. You will go to a page that asks about a donation, but you don't need to make one. Your download should begin automatically.
    • Install LibreOffice
      Once the installer is downloaded, double click on it and it should install.
    • To use LibreOffice, double click on the icon and it will open.
  2. Putty

    3. You will need a terminal program to access the AWS Cloud/HPC cluster.
    • Go to the Putty download page
    • Click on putty.exe link to download the install file
    • To use it, double-click on the downloaded file
    • Follow any installation instructions, if any
  3. FTP Client (Filezilla)

    4. An FTP client will help you transfer files easily between your computer and the cloud.
    • Go to the Filezila download page
    • Chose the download link appropriate to your system
    • To use it, double-click on the downloaded file
    • Follow any installation instructions, if any
    • At the workshop we will give you additional information (e.g. host, username, port) to connect
  4. IGV

    5. If time permits, we will use The Broad Institute's IGV (Integrated Genome Viewer) for looking at SAM and BAM files, SNPs, and variant calls.
    • To download IGV, please visit this page and log in. Please register if you do not already have a login.
    • Click on the large button for the Download Binary Distribution
    • Find the zip archive on your computer and expand it
    • To run IGV, double-click on the IGV.bat file.

Mac

Please go through all the installation steps below and make sure that you not only installed them, but start them up to make sure they're working. If you have any problems, don't hesitate to email the instructors to ask for help, or arrive early on the first day of the workshop to get help.

  1. A spreadsheet program

    2. For this workshop you will need a spreadsheet program. Many people already have Microsoft Excel installed, and if you do, you're set!
    If you need a spreadsheet program, there are a few other options, like OpenOffice and LibreOffice. Install instructions for LibreOffice, which is free and open source, are here.
    • Download the Installer
      Install LibreOffice by going to the installation page. The version for Mac should automatically be selected. Click Download Version 6.0.3 or later. You will go to a page that asks about a donation, but you don't need to make one. Your download should begin automatically.
    • Install LibreOffice
      Once the installer is downloaded, double click on it and it should install.
    • To use LibreOffice, double click on the icon and it will open.
  2. FTP Client (Filezilla)

    3. An FTP client will help you transfer files easily between your computer and the cloud.
    • Go to the Filezila download page
    • Chose the download link appropriate to your system
    • To use it, double-click on the downloaded file
    • Follow any installation instructions, if any
    • At the workshop we will give you additional information (e.g. host, username, port) to connect
  3. IGV

    4. If time permits, we will use The Broad Institute's IGV (Integrated Genome Viewer) for looking at SAM and BAM files, SNPs, and variant calls.</p>
    • To download IGV, please visit this page and log in. Please register if you do not already have a login.
    • Click on the large button for the Download Binary Distribution
    • Find the zip archive on your computer and expand it
    • To run IGV, double-click on the IGV.bat file.

Linux

Please go through all the installation steps below and make sure that you not only installed them, but start them up to make sure they're working. If you have any problems, don't hesitate to email the instructors to ask for help, or arrive early on the first day of the workshop to get help.

  1. A spreadsheet program

    2. For this workshop you will need a spreadsheet program. Many people already have Microsoft Excel installed, and if you do, you're set!
    If you need a spreadsheet program, there are a few other options, like OpenOffice and LibreOffice. Install instructions for LibreOffice, which is free and open source, are here.
    • Download the Installer
      Install LibreOffice by going to the installation page. The version for Linux should automatically be selected. Click Download Version 6.0.3 or later. You will go to a page that asks about a donation, but you don't need to make one. Your download should begin automatically.
    • Install LibreOffice
      Once the installer is downloaded, double click on it and it should install.
    • To use LibreOffice, double click on the icon and it will open.
  2. FTP Client (Filezilla)

    3. An FTP client will help you transfer files easily between your computer and the cloud.
    • Go to the Filezila download page
    • Chose the download link appropriate to your system
    • To use it, double-click on the downloaded file
    • Follow any installation instructions, if any
    • At the workshop we will give you additional information (e.g. host, username, port) to connect
  3. IGV

    4. If time permits, we will use The Broad Institute's IGV (Integrated Genome Viewer) for looking at SAM and BAM files, SNPs, and variant calls.
    • To download IGV, please visit this page and log in. Please register if you do not already have a login.
    • Click on the large button for the Download Binary Distribution.
    • Find the zip archive on your computer and expand it.
    • To run IGV, double-click on the IGV.bat file.