Infectious Disease Genomic Epidemiology

Install these tools before the workshop:

1) A robust text editor.

2) A file decompression tool.

  • For Windows/PC – 7zip.
  • For Linux – gzip.
  • For Mac – already there.

3) A robust internet browser such as Firefox or Safari (Internet Explorer and Chrome are not recommended because of Java issues).

4) SSH client - Mac and Linux users already have a command line ssh program that can be run from the terminal. For Windows users, please download PuTTY.

5) SCP/SFTP client - We will be moving data from the servers to the student laptops for visualization. Mac and Linux users already have a command line scp and sftp program. For Windows users, please install WinSCP.

6) A PDF viewer (Adobe Acrobat or equivalent).

7) GenGIS (http://kiwi.cs.dal.ca/GenGIS/Download).

Read these papers before the workshop:

General:
A Primer on Infectious Disease Bacterial Genomics
Bacterial population genetics, evolution and epidemiology
Impact of recombination on bacterial evolution

Antimicrobial Resistance:
CARD 2017
Antimicrobial resistance surveillance in the genomic age
MEGARes
Challenges and opportunities for whole-genome sequencing-based surveillance of antibiotic resistance

Phylogenomics:
SNVPhyl

Genome-based Multilocus Sequence Typing:
MLST in the genomic era
Whole Genome MLST

Phylogeography readings:
Ebola phylogeo analysis
Microreact
GenGIS 2.0
Haiti cholera

Do these tutorials before the workshop:

1) R Preparation tutorials: You are expected to have completed the following tutorials in R beforehand. The tutorial should be very accessible even if you have never used R before.

2) UNIX Preparation tutorials:

3) Sequencing Terminology

4) Download and install GenGIS (http://kiwi.cs.dal.ca/GenGIS/Download), and ideally report any problems they have installing or running the software. If you’re feeling ambitious, you can try out the tutorials that are accessible via http://kiwi.cs.dal.ca/GenGIS/Documentation.

5) PHYLOViZ Preparation tutorials: PHYLOViZ can be used for the analysis and visualization of data from sequence-based typing methods, including MLST in its various forms (MLST, rMLST, cgMLST, wgMLST, etc.) and SNP profiles. It can be used to visualize strain relationships using several clustering methods with colour coding based on epidemiological or other forms of ancillary data (i.e. “metadata”). There is a downloadable version as well as an online version. Make sure you check out the video tutorial. If you have time, read the walkthrough of features to get familiar with the user interface.