Computational Microbial Genomics project

Project for the course of Computational Microbial Genomics held by Professor Nicola Segata, Mireia Valles Colomer, and Francesco Asnicar (A.Y. 2022-2023).

Topic: Analysis of an uSGB

uSGB: SGB15132

Report

Set presentation slides

Authors

Project developed by:

• Andrea Tonina @iamandreatonina
• Gloria Lugoboni @GloriaLugoboni
• Lorenzo Santarelli @Lor-Santa

Tools

LINKS:

• iTol x phylogenetic trees
• Roary
• Phylo - Working with Phylogenetic Trees
• PhyloPhLan
• Prokka

Review

• Introduction
• Methods
• Results and Discussion
• Conclusions
• References

Lectures code update

• Genome annotation (prokka)
• Pangeonme analysis (roary)
• Taxonomic assignments (PhyloPhlan 3.0)
• Phylogenetic alignments
• Assosciation with host data