Summary and Setup

This is a new lesson built with The Carpentries Workbench.

Summary

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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

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You will use the same setup as for the Linux tutorial. See the corresponding page on Studium.

Data Sets

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Data for the molecular epidemiology part comes from Bryant et al., 2013