Working with Bacterial Genomes (IN-PERSON)

New

This comprehensive course equips you with essential skills and knowledge in bacterial genomics analysis, primarily using Illumina-sequenced samples. You'll gain an understanding of how to select the most appropriate analysis workflow, tailored to the genome diversity of a given bacterial species. Through hands-on training, you'll apply both de novo assembly and reference-based mapping approaches to obtain bacterial genomes for your isolates. You will apply standardised workflows for genome assembly and annotation, including quality assessment criteria to ensure the reliability of your results. Furthermore, you'll learn how to construct phylogenetic trees using whole genome and core genome alignments, enabling you to explore the evolutionary relationships among bacterial isolates. Lastly, you'll apply methods to detect antimicrobial resistance genes. As examples we will use Mycobacterium tuberculosis, Staphylococcus aureus and Streptococcus pneumoniae, allowing you to become well-equipped to conduct bacterial genomics analyses on a range of species.

If you do not have a University of Cambridge Raven account please book or register your interest here.

• ♿ The training room is located on the first floor and there is currently no wheelchair or level access.
• Our courses are only free for registered University of Cambridge students. All other participants will be charged according to our charging policy.
• Attendance will be taken on all courses and a charge is applied for non-attendance, including for University of Cambridge students. After you have booked a place, if you are unable to attend any of the live sessions, please email the Bioinfo Team.
• Further details regarding eligibility criteria are available here.

The course is aimed at biologists interested in microbiology, prokaryotic genomics and antimicrobial resistance.

Essential

• Basic understanding of high-throughput sequencing technologies.
  • Watch this iBiology video for an excellent overview.
• A working knowledge of the UNIX command line (course registration page).
  • If you are not able to attend this prerequisite course, please work through our Unix command line materials ahead of the course (up to section 7).
• A working knowledge of R (course registration page).
  • If you are not able to attend this prerequisite course, please work through our R materials ahead of the course.

Desirable

• A basic knowledge of phylogenetics inference methods (course registration page).
• A working knowledge of running analysis on High Performance Computing (HPC) clusters (course registration page).

Number of sessions: 5

Bioinformatics, Data visualisation, Data handling, Bacterial genomics, Antimicrobial resistance, Phylogenetics, Pathogen surveillance

By the end of this course, you will be able to:

• Choose the most suitable analysis workflow based on the genome diversity of a given bacterial species.
• Differentiate between "de novo assembly" and "reference-based mapping" approaches for reconstructing bacterial genomes.
• Apply standardised workflows to assemble and annotate genomes using both approaches.
• Evaluate the quality of assembled genomes and determine their suitability for downstream analysis.
• Detect and remove recombinant regions.
• Construct phylogenetic trees using both whole genome and core genome alignments.
• Detect the presence of antimicrobial resistance genes in your isolates.

During this course you will learn about:

• Utilising standardised Nextflow workflows designed for bacterial genomics.
• Conducting quality control of raw sequencing data using the avantonder/bacQC pipeline.
• Performing de novo genome assembly, annotation, and quality assessment using the avantonder/assembleBAC pipeline.
• Creating whole genome multiple sequence alignments with nf-core/bactmap and core genome sequence alignments using Panaroo.
• Identifying and removing recombinant regions with Gubbins.
• Building maximum likelihood phylogenetic trees with IQ-Tree.
• Conducting antimicrobial resistance (AMR) analysis with species-specific tools (TB-Profiler), online tools (Pathogenwatch) and the nf-core/funcscan pipeline.

Presentations, demonstrations and practicals

Under revision

• Free for registered University of Cambridge students
• £ 60/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
• It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
• £ 60/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
• £ 120/day for all Industry participants. These charges must be paid at registration
• Further details regarding the charging policy are available here

5

once per year