Microbial Genomics: evolution, phylogenetics, and molecular epidemiology: Key Points

NCBI

NCBI website is very, very comprehensive
The Entrez cross-referencing system helps retrieving links bits of data of different type.

The simplest of the trees are distance-based.
UPGMA works by clustering the two closest leaves and recalculating the distance matrix.
Neighbor-joining is distance-based and fast, but not necessarily very accurate
Maximum-likelihood is slower, but more accurate

Random genetic drift has a large influence on the probability of fixation of alleles in small populations, even for non-neutral alleles.
Random genetic drift has very little influence of the probability of fixation of alleles in large populations.
Slightly deleterious mutations can get fixed into the population through random genetic drift, if the population is small enough and the selective value is not too large.

wget is a computer program to get data from the internet
for loops let you perform the same set of operations on multiple files with a single command
Sequencing data is large
In bioinformatic workflows the output of one tool is the input of the other.
FastQC is used to judge the quality of sequencing reads.
Data cleaning is an essential step in a genomics pipeline.
We will work towards confirming or disputing transmission in TB cases
After this practical training you will have some familiarity with working on the command line

Assembly is a process which aligns and merges fragments from a longer DNA sequence in order to reconstruct the original sequence.
k-mers are short fragments of DNA of length k

Single nucleotide polymorphisms can be identified by mapping reads to a reference genome
Parameters for the analysis have to be selected based on expected outcomes for this organism
Concatenation of SNPs helps to reduce analysis volume
Phylogenetic trees can be written with a bracket syntax in Newick format

SNP phylogeny and metadata can convey different messages
Human interpretation is often needed to weigh the different information sources.
The low mutation rate of M. tuberculosis does not allow to make confident inferences of transmission but does allow to exclude transmission