Salmonella genomic epidemiology exercise

Adapted by Lauren Cowley from original PHE training material by Philip Ashton and Tim Dallman Answers at the end Salmonella Enteritidis PT14b outbreak exercise Bioinformatics training, interpretation of phylogenies Prepared by the Gastrointestinal, Emerging and Zoonotic Infections department and the Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London.   Aim of Session To develop…

Guideline to bioinformatics tools

Quality Assessment and Trimming Trimmomatic http://www.usadellab.org/cms/index.php?page=trimmomatic Trimmomatic: A flexible trimmer for Illumina Sequence Data.┬áBolger, A. M., Lohse, M., & Usadel, B. (2014). Bioinformatics, btu170. A flexible read trimming tool that will remove Illumina adapters, reads below a certain length and low quality ends of the read Seqtk https://github.com/lh3/seqtk Tool for processing sequences in the FASTA…