Exercise

EXERCISE IS UNDER CONSTRUCTION

Introduction

Dear course participants,

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

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 zcat to read the first lines of one of the files to see some of the file content.

EX02 What species is it ?

The laboratory have sequenced genomic DNA from single colony isolates of bacteria cultivated from a clinical specimen. The sequence reads have been de novo assembled and genome assemblues have been stored in FASTA-formatted files: X

You want to determine the bacterial species of the genomes. You can use the Genome Taxonomy Database (GTDB) to determnine the species of the genomes.

https://teaching.healthtech.dtu.dk/22126/index.php/File:Gtdbtk.pdf