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

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.

Reference

GTDB-Tk tutorial (PDF)