Course Overview
Course Integrity
This course is compiled automatically on 2021-03-23
The course is tested and available on MacOS, Windows and Ubuntu Linux for R version 4.0.3 (2020-10-10)
Overview
This is a 6-hour course on Genome Sequencing and Assembly held at the Rockefeller University in March 2021.
The course consists of 2 sessions. These sessions will walk you through the core principles of Genome Assembly. Practical exercises will be performed using the web interface Galaxy.
Course material and exercises are available to view as rendered HTML at https://rockefelleruniversity.github.io/GenomeAssembly/. All material is available to download under GPL v2 license.
Setting up
System Requirements
Set Up Galaxy
Galaxy is a free, public, internet accessible data analysis resource. It allows access to various bioinformatics tools and workflows through a web browser.
Please create your free Galaxy account before the course begins. Ensure you use the EU mirror (which is found by following the link), as it is more stable. You can find extensive documentation on Galaxy here.
Install R
R can be installed from the R-project website.
The R website can be found here http://www.r-project.org/.
The download links and associated installation instructions for multiple platforms can be found below provided by Revolution Analytics. https://cran.revolutionanalytics.com
We recommend installing R 4.0.3 as this is the version used to compile the course. Direct downloads for R 4.0.3 for the main platforms can be found below:
Install Slack
We will be using a custom Slack channel to provide support as you assemble genomes with Galaxy.
You can use Slack through a web browser or you can install the Desktop app. Go to the Slack website to set up an account.
Once you have an account join our Slack channel here.
Install required packages
From the course package
install.packages('BiocManager')
BiocManager::install('RockefellerUniversity/GenomeAssembly')From CRAN and Bioconductor
install.packages('BiocManager')
BiocManager::install('methods')
BiocManager::install('ggplot2')
BiocManager::install('rmarkdown')
BiocManager::install('rio')
BiocManager::install('knitr')
BiocManager::install('testthat')
BiocManager::install('yaml')The Presentations
Genome Assembly, Session 1
In this session we will overview the principles of Genome Assembly.
Links to presentations:
The html slide presentation can be found at this link Slide
The single page html presentation can be found at this link Single Page
The code use in the presentations can be found at R code
Genome Assembly, Session 2
In this session we will review the practical use of Galaxy for Genome Assembly detailed in the exercise.
Links to presentations:
The html slide presentation can be found at this link Slide
The single page html presentation can be found at this link Single Page
The code use in the presentations can be found at R code
Getting help
Course help
For advice, help and comments for the material covered in this course please contact us at the issues page associated to this course.
The link to the help pages can be found here
General Bioinformatics support
If you would like contact us about general bioinformatics advice, support or collaboration, please contact us the Bioinformatics Resource Center at brc@rockefeller.edu.