Exercise - Revision history

Mick at 15:41, 12 January 2026

2026-01-12T15:41:47Z

← Older revision		Revision as of 17:41, 12 January 2026
Line 32:		Line 32:

	<p>		<p>
	~~Create an~~ object ~~containing~~ a Newick ~~tree~~:		This is how you create a phylogenetic tree object in R from a Newick string:
	</p>		</p>

Mick at 07:50, 11 January 2026

2026-01-11T07:50:14Z

← Older revision		Revision as of 09:50, 11 January 2026
Line 90:		Line 90:
	<pre>		<pre>
	# Read data		# Read data
	unaligned_mars <- read.FASTA("marsupials_unaligned.fasta")		unaligned_mars <- read.FASTA("/home/projects/22126_NGS/exercises/phylogenomics/marsupials_unaligned.fasta")
	aligned_mars <- as.matrix(read.FASTA("marsupials_aligned.fasta"))		aligned_mars <- as.matrix(read.FASTA("/home/projects/22126_NGS/exercises/phylogenomics/marsupials_aligned.fasta"))

	###########################		###########################
Line 167:		Line 167:
	<pre>		<pre>
	# Run maximum-likelihood with a very simple model		# Run maximum-likelihood with a very simple model
	system("/home/ctools/iqtree-3.0.1-Linux/bin/iqtree3 -s marsupials_aligned.fasta -m JC -bb 1000 -pre mars_jc")		system("/home/ctools/iqtree-3.0.1-Linux/bin/iqtree3 -s /home/projects/22126_NGS/exercises/phylogenomics/marsupials_aligned.fasta -m JC -bb 1000 -pre mars_jc")

	# Run maximum-likelihood with a more complex model		# Run maximum-likelihood with a more complex model
	system("/home/ctools/iqtree-3.0.1-Linux/bin/iqtree3 -s marsupials_aligned.fasta -m GTR+R6 -bb 1000 -pre mars_gtr")		system("/home/ctools/iqtree-3.0.1-Linux/bin/iqtree3 -s /home/projects/22126_NGS/exercises/phylogenomics/marsupials_aligned.fasta -m GTR+R6 -bb 1000 -pre mars_gtr")
	</pre>		</pre>

Line 238:		Line 238:

	<pre>		<pre>
	mars_trs <- read.tree("marsupials.tree")		mars_trs <- read.tree("/home/projects/22126_NGS/exercises/phylogenomics/marsupials.tree")

	# Plot 9 randomly chosen trees from the set		# Plot 9 randomly chosen trees from the set

Mick at 07:47, 11 January 2026

2026-01-11T07:47:45Z

← Older revision		Revision as of 09:47, 11 January 2026
Line 26:		Line 26:

	<pre>		<pre>
	library(ape)		library(ape, lib.loc = "/home/ctools/Rlibs")
	library(strap)		library(strap, lib.loc = "/home/ctools/Rlibs")

	</pre>		</pre>

Mick at 07:43, 11 January 2026

2026-01-11T07:43:39Z

← Older revision		Revision as of 09:43, 11 January 2026
Line 166:		Line 166:
	<pre>		<pre>
	# Run maximum-likelihood with a very simple model		# Run maximum-likelihood with a very simple model
	system("iqtree3 -s marsupials_aligned.fasta -m JC -bb 1000 -pre mars_jc")		system("/home/ctools/iqtree-3.0.1-Linux/bin/iqtree3 -s marsupials_aligned.fasta -m JC -bb 1000 -pre mars_jc")

	# Run maximum-likelihood with a more complex model		# Run maximum-likelihood with a more complex model
	system("iqtree3 -s marsupials_aligned.fasta -m GTR+R6 -bb 1000 -pre mars_gtr")		system("/home/ctools/iqtree-3.0.1-Linux/bin/iqtree3 -s marsupials_aligned.fasta -m GTR+R6 -bb 1000 -pre mars_gtr")
	</pre>		</pre>

Mick at 07:35, 11 January 2026

2026-01-11T07:35:32Z

Show changes

Rasmus: Replaced content with "x"

2026-01-06T11:57:56Z

Replaced content with "x"

← Older revision		Revision as of 13:57, 6 January 2026
Line 1:		Line 1:
			x

	~~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:~~

	~~<pre>~~
	~~zcat filename.fastq.gz \| head~~
	~~</pre>~~

	~~== 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 ===~~

	~~[https://teaching.healthtech.dtu.dk/22126/images/c/cd/Gtdbtk.pdf GTDB-Tk tutorial (PDF)]~~

Rasmus at 11:54, 6 January 2026

2026-01-06T11:54:00Z

← Older revision		Revision as of 13:54, 6 January 2026
Line 1:		Line 1:

	~~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~~

Rasmus at 11:53, 6 January 2026

2026-01-06T11:53:00Z

← Older revision		Revision as of 13:53, 6 January 2026
Line 63:		Line 63:
	=== Reference ===		=== Reference ===

	[https://teaching.healthtech.dtu.dk/22126/~~index.php~~/~~File:~~Gtdbtk.pdf GTDB-Tk tutorial (PDF)]		[https://teaching.healthtech.dtu.dk/22126/images/c/cd/Gtdbtk.pdf GTDB-Tk tutorial (PDF)]

Rasmus at 11:51, 6 January 2026

2026-01-06T11:51:28Z

← Older revision		Revision as of 13:51, 6 January 2026
Line 27:		Line 27:

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

			<pre>
			zcat filename.fastq.gz \| head
			</pre>

			== 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 ===

			[https://teaching.healthtech.dtu.dk/22126/index.php/File:Gtdbtk.pdf GTDB-Tk tutorial (PDF)]

Rasmus at 11:50, 6 January 2026

2026-01-06T11:50:28Z

← Older revision		Revision as of 13:50, 6 January 2026
Line 25:		Line 25:

	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.		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