Data processing and visualization for metagenomics


1-2 July 2021

9:30 am - 5:00 pm

Instructors: Marc Galland1, Jesse Kerkvliet3, Rodrigo Meneses3, Misha Paauw1, Anouk Zancarini1

Helpers: Stacy Shinneman2, Rodrigo Meneses3, Jesse Kerkvliet3

1: SILS institute, 2: IBED institute, 3: UMC Utrecht

Data processing and visualization for metagenomics.

General Information


This lesson will introduce you to data processing and visualization for shotgun metagenomics. Contrarily to amplicon-based metagenomics, this technique can yield whole microbial genomes from environmental samples. This is helpful as reconstructing microbial genomes can give an insight into their functional gene repertoire. Still, shotgun metagenomics comes with its own challenges mostly in terms of cost and computional challenges. This workshop is meant to provide with a clear, stable starting point to perform a shotgun metagenomics experiment and visualise the results.

This workshop is part of the 2021 Summer School organised by the Amsterdam Science Park Study Group. This event is made possible thanks to the support of the NWO Team Science Award (2020 edition).

Who are we

This workshop is organized by the core members of the Amsterdam Science Park Study Group. This small community of computational biologists aims to promote skill sharing and collaboration through the organisation of interactive workshops. It acts as the main local hub to set-up Software and Data Carpentry workshops (official workshops and Carpentry-style). All are welcome to this study group, regardless of scientific research area, affiliation or training level.

For more information on what we teach and why, see our website: "scienceparkstudygroup".




Who: The course is aimed at master students and other researchers (PhD. and postdoc). You will need to have basic knowledge of the command-line (Shell). You can follow the [Introduction to programming in Python workshop](https://scienceparkstudygroup.github.io/Intro-Python-workshop/) to gain this required knowledge.

Where: Online, Amsterdam UTC+1 (see Zoom links). Get directions with OpenStreetMap or Google Maps.

Zoom links: the workshop will be fully online:

When: 1-2 July 2021. Add to your Google Calendar.

Requirements: Participants must dispose of 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).

Code of Conduct: Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Helpers: Experts helping in the room.:

Schedule

Day 1

Morning
(9:30-11:00)		 Starting a metagenomics project
(Anouk)
Coffee break :coffee:
Morning
(11:15-12:45)		 Assessing Read Quality
Trimming and filtering
(Misha - Marc)
Lunch break :pizza:
Afternoon
(13:45-15:15)		 Metagenome assembly
Metagenome Binning
(Jesse - Marc)
Tea break :tea:
Afternoon
(15:30-17:00)		 Taxonomic Assignment
(Anouk - Rodrigo)

Day 2

Morning
(9:30-11:00)		 Diversity tackled with R
(Anouk - Rodrigo)
Coffee break :coffee:
Morning
(11:15-12:45)		 Taxonomic Analysis
with R
(Anouk - Rodrigo)
Lunch break :pizza:
Afternoon
(13:45-15:15)		 Other resources
(Anouk)
Tea break :tea:
Afternoon
(15:30-17:00)		 Conclusions
Q&As
(Anouk)

Discord server: We will use Discord to manage questions, general announcements and to match helpers with learners. Please install the Discord application on your laptol/computer. The invite link to the server can be found under this link There are several channels that we will use:




Contact: Please email m.galland@uva.nl for more information.





Syllabus

Introduction to the Command Line

Introduction to R

Version Control with Git

  • Creating a repository
  • Configuring Git
  • Recording Changes to Files: add, commit, ...
  • Viewing State Changes with status
  • Working on the Web: clone, pull, push, ...
  • Where to Host Work, and Why
  • Reference...


Setup

To participate in a this workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.


Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser.

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

Git should be installed on your computer as part of your Bash install (described above).

Video Tutorial

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.


Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Others editors that you can use are BBEdit or Sublime Text.

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.


R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Video Tutorial

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo dnf install R). Also, please install the RStudio IDE.