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.
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 it?
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:
- X
Task
Your goal is to determine the bacterial species of the assembled genomes.
You can use the Genome Taxonomy Database (GTDB) to determine the species assignment.