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2023 Workshop details
Workshop #1) March 2, 2023
| Title | Introduction to the 2023 MMID Bioinformatics Workshop |
|---|---|
| Instructor | Grace E. Seo |
| Time | 9:15 AM - 10:15 AM |
Workshop Information For in-person attendees
- Setup U of M Wi-Fi connection
For all attendees
- Enable WSL (Windows user)
- Install Ubuntu (BASH)
- Install R and RStudio
- Setup GitHub account and provide brief overview on file download
- Provide useful starter guides on BASH and R
- Provide Galaxy Training links
Workshop #2) March 9, 2023
| Title | Introduction to conda and tool installation |
|---|---|
| Instructor | Grace E. Seo |
| Time | 9:15 AM - 10:15 AM |
Workshop Information
- Overview of conda (concept and purpose explanation)
- Install conda environment
- Install bioinformatics tools as conda package
Workshop #3) March 16, 2023
| Title | Introduction to Genomics and Viral data analysis |
|---|---|
| Instructor | Grace E. Seo |
| Time | 9:15 AM - 10:15 AM |
Workshop Information
- Overview of virus genome dataset (note that bacterial genome dataset is next week)
- long read vs. short read sequencing
- Publicly available genome sequence dataset retrieval (GISAID, VirusSeq, NCBI)
- Write a basic script to analyze data using useful bioinformatics tools
Workshop #4) March 23, 2023
| Title | Bacterial Genomics |
|---|---|
| Instructor | Jill Rumore |
| Time | 9:15 AM - 10:15 AM |
Workshop Information
- workflow from qc to read classification
- overview of commonly used tools (i.e., fastqc, fastp, bowtie2, checkM)
- install conda program (i.e., fastp and/or checkM)
- assess publically available dataset for quality using the installed tool
This workshop will provide demonstrations and exercises for performing basic bioinformatics analysis of bacterial genomic data as it pertains to quality control and data preprocessing, which are critical to obtaining high-quality data for downstream data analysis. Specifically, we will assess general data quality using FastQC, filter low quality reads using fastp and remove host sequence content using a combination of Bowtie 2 and samtools. We will also explore the use of checkM to assess the completeness and contamination of bacterial genome assemblies.
Workshop #5) March 30, 2023
| Title | Reference databases |
|---|---|
| Instructor | Jill Rumore |
| Time | 9:15 AM - 10:15 AM |
Workshop Information
- What makes a good reference database?
- Where to find publically available reference databases
- Download publically available reference database
- Perform read classification
- Briefly touch on interpretation (time permitting)
Workshop #6) April 6, 2023
| Title | Beginner’s Guide to Phylogenetic Trees |
|---|---|
| Instructor | Taylor Davedow |
| Time | 9:15 AM - 10:15 AM |
Workshop Information Examples of linux based tools (might not be covered)
- IQtree - maximum likelihood
- mashtree - rapid comparison of WGS (does not infer phylogeny)
- Fasttree - approximate MLT
- phyML - maximum likelihood
- Quicktree - neighbour-joining
Web-based tools to quickly view output
- iTol
- Phandango
- Auspice
Workshop #7) April 13, 2023
| Title | Introduction to tree visualization and annotation using ggtree |
|---|---|
| Instructor | Taylor Davedow |
| Time | 9:15 AM - 10:15 AM |
Workshop Information
- Interactive tree visualization using RStudio
Workshop #8) April 20, 2023
| Title | Bfx workshop: Bring your own dataset! |
|---|---|
| Time | 9:15 AM - 10:15 AM |
Workshop Information
- Attendees are encouraged to work with each other to analyze their data. Very limited number of volunteers will be available to provide individual guide on data analysis.
Workshop #9) April 27, 2023
| Title | Bfx workshop: Bring your own dataset! |
|---|---|
| Time | 9:15 AM - 10:15 AM |
Workshop Information
- Attendees are encouraged to work with each other to analyze their data. Very limited number of volunteers will be available to provide individual guide on data analysis.
© MMID Bioinformatics Workshop 2023