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Comparative Genomics

Week beginning November 18th 2024

Instructors and assistants:

  • Dr Gemma Langridge (lead): Gemma.Langridge@quadram.ac.uk
  • Dr Emma Waters
  • Alice Nisbet
  • Eleanor Hayles

Required software To be installed in new Conda environment compgen

conda create --name compgen
conda activate compgen
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
conda install prokka
conda install socru
conda install breseq
conda install refseq_masher
conda install mlst
conda install snippy
conda install sistr_cmd
conda install shovill
conda install roary
conda install artemis
conda install scoary

Monday November 18th

Venue: UG55B

Topic: Mapping and variant calling (slides)

Dataset: A set of Salmonella enterica serovar Typhi samples that have been sequenced

Tasks:

  • Compare the results of using short and long read sequencing to map to a reference.
  • What is similar, what is different and what impact does this have on the overall interpretation?
  • What isn’t included when you do analysis using a reference genome?
  • Is it important and what does it do?
  • How do you choose a reference to use?

Schedule:

9:00-10:00 – Introduction and setup of task; installation of software
10:00-12:00 – Task
13:00- 15:00 – Task
15:00-16:00 – Talk from UKHSA
16:00-17:00 – Wrap up

Tuesday November 19th

Venue: UG55B

Topic: Pan-genomes and mobile genetic elements (slides)

Tasks:

  • Construct a pan-genome of the dataset from Monday.
  • What is core to all of the genomes and what is accessory.
  • What is actually in the accessory genome, what do the genes do and why does it matter?
  • How do you tell between a mis-assembly, an integron, a plasmid etc…

Schedule:

9:00-10:00 – Introduction and setup of task
10:00-12:00 – Task
13:00-15:00 - Task
15:00-16:00 – Wrap up

Wednesday November 20th

Venue: UG44A

Topic: Genome comparison (slides)

Tasks:

  • Can you identify and visualise large structural variation?
  • Why is this important?
  • Can you identify large insertions and deletions?
  • What genes are impacted?
  • Can you distinguish between an informatics artefact and a real signal?

Schedule:

9:00-10:00 – Introduction and setup of task
10:00-12:00 – Task
13:00-15:00 - Task
15:00-15:30 – Talk from Dr Emma Waters
15:30-16:30 – Wrap up

Friday November 22nd

Venue: UG55B

Topic: Outbreak investigation (slides)

Dataset:

| biosample_acc | strain       | genBankAssembly | SRArun_acc |
|---------------|--------------|-----------------|------------|
| SAMN00860590  | CFSAN000191  | GCA_000698635.1 | SRR498369  |
| SAMN00862340  | CFSAN000228  | GCA_000748565.1 | SRR500493  |
| SAMN00862341  | CFSAN000212  | GCA_000748245.1 | SRR500494  |
| SAMN00989085  | CFSAN000211  | GCA_000698715.1 | SRR498373  |
| SAMN00991042  | CFSAN000661  | GCA_000698515.1 | SRR498397  |
| SAMN00991044  | CFSAN000669  | GCA_000749005.1 | SRR498399  |
| SAMN00991046  | CFSAN000700  | GCA_000749045.1 | SRR498402  |
| SAMN00991047  | CFSAN000752  | GCA_000749065.1 | SRR498403  |
| SAMN00991048  | CFSAN000753  | GCA_000749085.1 | SRR498404  |
| SAMN01816351  | CFSAN001118  | GCA_000748065.1 | SRR1258443 |
| SAMN01816352  | CFSAN001140  | GCA_000748085.1 | SRR1258440 |
| SAMN01816358  | CFSAN001112  | GCA_000748025.1 | SRR1258439 |
| SAMN01816359  | CFSAN001115  | GCA_000748045.1 | SRR1258442 |
| SAMN01823701  | CFSAN000189  | GCA_000439415.1 | SRR498276  |
| SAMN01942233  | CFSAN000951  | GCA_000749145.1 | SRR498422  |
| SAMN01942244  | CFSAN000954  | GCA_000748405.1 | SRR498425  |
| SAMN01942246  | CFSAN000963  | GCA_000749295.1 | SRR498436  |
| SAMN01942253  | CFSAN000961  | GCA_000748525.1 | SRR498434  |
| SAMN01942254  | CFSAN000960  | GCA_000748505.1 | SRR498433  |
| SAMN01942268  | CFSAN000968  | GCA_000698535.1 | SRR498442  |
| SAMN01942296  | CFSAN000970  | GCA_000749415.1 | SRR498444  |
| SAMN01942300  | CFSAN000958  | GCA_000748465.1 | SRR498431  |
| SAMN01942313  | CFSAN000952  | GCA_000749165.1 | SRR498423  |

Tasks:

  • This is a dataset from a real outbreak investigation. Time is critical.
  • Are the samples linked?
  • What information can you find out about these samples to aid the epidemiologists?

Schedule:

9:00-9:15 – Introduction and setup of task
9:15-11:30 – Task
11:30-12:30 – Wrap up