Microbial genomics exercise

Dear course participants,

In this exercise you will analyse microbial genome sequences using bioinformatics tools that are commonly used for microbial diagnostics and research.

The tools are available at the server as Apptainer container images. Although the image files are located in /home/projects/microbial_genomics/singularity_image_files, you do not need to call them directly. Instead, you can run the tools using the provided BASH executables in /home/ctools/bin, which is already available via your $PATH.

gtdbtk.sh
mlst.sh
parsnp.sh
abricate.sh

You can use

Background

We imagine that we are employed at a hospital to provide diagnostics for patient care.

The laboratory has sequenced genomic DNA from a clinical specimen. The sequence reads are stored in FASTQ files that are compressed with gzip:

• X
• Y

Use the following command to read the first lines of one of the files and inspect its content:

zcat filename.fastq.gz | head

EX02: What species is the genome ?

The laboratory has sequenced genomic DNA from single-colony isolates of bacteria cultivated from a clinical specimen. The sequence reads have been de novo assembled, and the genome assemblies are stored in FASTA-formatted files available in /home/projects/microbial_genomics/genome_assemblies.

Your want to determine the bacterial species of the assembled genomes.

We can use the GTDB-Tk tool to assign taxonomic classifications to bacterial genomes based on the Genome Database Taxonomy (GTDB).

Run gtdbtk.sh -h to get help information on how to use GTDB-Tk.

Use GTDB-Tk to determine the species of the genomes:

gtdbtk.sh classify_wf --extension .fna --cpus 10 --genome_dir /home/projects/microbial_genomics/ex02_assemblies --out_dir $HOME/output

Question: What species are the genomes ?

Supplementary files

Article describing GTDB-Tk can be found here