A bacterial genome assembly and annotation laboratory using a virtual machine

Ellina Trofimova, Shahla Asgharzadeh Kangachar, Karen D. Weynberg, Robert D. Willows, Paul R. Jaschke*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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Abstract

With the global increase of infections caused by antibiotic-resistant bacterial strains, there is an urgent need for new methods of tackling the issue. Genomic analysis of bacterial strains can help to understand their virulence and antibiotic resistance profile. Bioinformatic skills are in great demand across the biological sciences. We designed a workshop that allows university students to learn the process of genome assembly using command-line tools within a virtual machine on a Linux operating system. We use Illumina and Nanopore short and long-read raw sequences to reveal the advantages and disadvantages of short, long, and hybrid assembly methods. The workshop teaches how to assess read and assembly quality, perform genome annotation, and analyze pathogenicity, antibiotic and phage resistance. The workshop is intended for a five-week teaching period and is concluded by a student poster presentation assessment.

Original languageEnglish
Pages (from-to)276-285
Number of pages10
JournalBiochemistry and Molecular Biology Education
Volume51
Issue number3
Early online date3 Mar 2023
DOIs
Publication statusPublished - May 2023

Bibliographical note

Copyright the Author(s) 2023. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

Keywords

  • bacterial immunity
  • bacteriophage
  • genome annotation
  • phage therapy
  • UPEC

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