Summary and Schedule
This is a new lesson built with The Carpentries Workbench.
| Setup Instructions | Download files required for the lesson | |
| Duration: 00h 00m | 1. NCBI |
How do you efficiently and reliably navigate NCBI’s
website? How do you search sequences? How do you use the right BLAST flavor? |
| Duration: 04h 00m | 2. BLAST |
How to use the command-line version of BLAST?
|
| Duration: 08h 00m | 3. Multiple sequence alignment |
How do you align multiple sequences? Why is it important to properly align sequences? |
| Duration: 10h 00m | 4. Phylogenetics |
How do you build a simple, distance-based phylogenetic tree? How do you build a phylogenetic tree with more advanced methods? How do you ascertain statistical support for phylogenetic trees? |
| Duration: 13h 00m | 5. Reads, QC and trimming |
Trace an outbreak of Mycobacterium, from reads to phylogenetic
tree. How can I organize my file system for a new bioinformatics project? How and where can data be downloaded? How can I describe the quality of my data? How can I get rid of sequence data that doesn’t meet my quality standards? |
| Duration: 15h 30m | 6. Sequence assembly |
How can the information in the sequencing reads be reduced? What are the different methods for assembly? |
| Duration: 19h 30m | 7. Mapping | How to generate a phylogenetic tree from SNP data? |
| Duration: 23h 30m | 8. Molecular epidemiology |
How are phylogenetic trees viewed and compared? How can I visualize several layers of data? In which cases is transmission likely? |
| Duration: 03h 30m | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.
Summary
These pages contain instructions for computer lab part of the lectures on microbial evolution and epidemiology. The exercises are to be performed either on a web browser or on Uppmax.
In the first 2 episodes, you’ll be mostly working on web-based exercises. In episodes 3-4, you’ll practice multiple sequence alignment and building phylogenies, based on single genes.
Episodes 5-9 explore, with real data, an outbreak of tuberculosis, going from raw reads to inferring hypotheses about transmission.
Software Setup
You will use the same setup as for the Linux tutorial. See the corresponding page on Studium.
Data Sets
Data for the molecular epidemiology part comes from Bryant et al., 2013