Microbial genomics exercise - Revision history

Rasmus at 13:12, 12 January 2026

2026-01-12T13:12:14Z

← Older revision		Revision as of 15:12, 12 January 2026
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	==== Solution ====		==== Solution ====
	Yes, some genomes from different persons have pairwise SNP-distances that are low relative the the distances between genomes from the same person. A quick search for information on the world wide web may suggest that for ''Pseudomonas aeruginosa'', SNP-distances less than around 30 SNPs indicates transmission at the hospital.		Yes, some genomes from different persons have pairwise SNP-distances that are low relative to the the distances between genomes from the same person. A quick search for information on the world wide web may suggest that for ''Pseudomonas aeruginosa'', SNP-distances less than around 30 SNPs indicates transmission at the hospital.

	</div>		</div>

Rasmus at 12:58, 12 January 2026

2026-01-12T12:58:32Z

← Older revision		Revision as of 14:58, 12 January 2026
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	Unfortunately, GTDK-Tk uses a lot of memory, so it is not feasible to run the tool at the course servers. Instead, the following command has already been to determine the species of the genomes and the results have been moved to <code>/home/projects/microbial_genomics/premade_task_results_from_teacher</code>:		Unfortunately, GTDK-Tk uses a lot of memory, so it is not feasible to run the tool at the course servers. Instead, the following command has already been to determine the species of the genomes and the results have been moved to <code>/home/projects/microbial_genomics/premade_task_results_from_teacher</code>:
	<pre>		<pre>
	gtdbtk.sh classify_wf --extension .fna --cpus 10 --genome_dir /home/projects/microbial_genomics/task02_assemblies --out_dir ~/microbial_exercise/output_gtdb		DO NOT RUN THIS gtdbtk.sh classify_wf --extension .fna --cpus 10 --genome_dir /home/projects/microbial_genomics/task02_assemblies --out_dir ~/microbial_exercise/output_gtdb DO NOT RUN THIS
	</pre>		</pre>

Rasmus: /* Task02: Species-level taxonomic classification of bacterial genomes */

2026-01-12T10:05:30Z

Task02: Species-level taxonomic classification of bacterial genomes

← Older revision		Revision as of 12:05, 12 January 2026
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	Run <code>gtdbtk.sh -h</code> to get help information on how to use GTDB-Tk.		Run <code>gtdbtk.sh -h</code> to get help information on how to use GTDB-Tk.

	Unfortunately, GTDK-Tk uses a lot of memory, so it is not feasible to run the tool at the course servers. Instead, the following command has already been to determine the species of the genomes and the results have been moved to <code>/home/projects/microbial_genomics/~~premade_task_results/output_gtdb_from_teacher~~</code>:		Unfortunately, GTDK-Tk uses a lot of memory, so it is not feasible to run the tool at the course servers. Instead, the following command has already been to determine the species of the genomes and the results have been moved to <code>/home/projects/microbial_genomics/premade_task_results_from_teacher</code>:
	<pre>		<pre>
	gtdbtk.sh classify_wf --extension .fna --cpus 10 --genome_dir /home/projects/microbial_genomics/task02_assemblies --out_dir ~/microbial_exercise/output_gtdb		gtdbtk.sh classify_wf --extension .fna --cpus 10 --genome_dir /home/projects/microbial_genomics/task02_assemblies --out_dir ~/microbial_exercise/output_gtdb
	~~mv ~/microbial_exercise/output_gtdb /home/projects/microbial_genomics/premade_task_results/output_gtdb_from_teacher~~
	</pre>		</pre>

Rasmus at 09:46, 12 January 2026

2026-01-12T09:46:17Z

← Older revision		Revision as of 11:46, 12 January 2026
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	Run <code>gtdbtk.sh -h</code> to get help information on how to use GTDB-Tk.		Run <code>gtdbtk.sh -h</code> to get help information on how to use GTDB-Tk.

	Unfortunately, GTDK-Tk uses a lot of memory, so it is not feasible to run the tool at the course servers. Instead, the following command has already been to determine the species of the genomes and the results have been moved to <code>/home/projects/microbial_genomics/premade_task_results</code>:		Unfortunately, GTDK-Tk uses a lot of memory, so it is not feasible to run the tool at the course servers. Instead, the following command has already been to determine the species of the genomes and the results have been moved to <code>/home/projects/microbial_genomics/premade_task_results/output_gtdb_from_teacher</code>:
	<pre>		<pre>
	gtdbtk.sh classify_wf --extension .fna --cpus 10 --genome_dir /home/projects/microbial_genomics/task02_assemblies --out_dir ~/microbial_exercise/output_gtdb		gtdbtk.sh classify_wf --extension .fna --cpus 10 --genome_dir /home/projects/microbial_genomics/task02_assemblies --out_dir ~/microbial_exercise/output_gtdb
	mv ~/microbial_exercise/output_gtdb /home/projects/microbial_genomics/premade_task_results/.		mv ~/microbial_exercise/output_gtdb /home/projects/microbial_genomics/premade_task_results/output_gtdb_from_teacher
	</pre>		</pre>

Rasmus: /* Task05: Detection of antimicrobial resistance genes */

2026-01-11T21:43:33Z

Task05: Detection of antimicrobial resistance genes

← Older revision		Revision as of 23:43, 11 January 2026
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	Are the same AMR genes found in the five genomes ?		Are the same AMR genes found in the five genomes ?

			<div class="mw-collapsible mw-collapsed">

	==== Solution ====		==== Solution ====

Rasmus at 21:42, 11 January 2026

2026-01-11T21:42:52Z

← Older revision		Revision as of 23:42, 11 January 2026
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	==== Question 1 ====		==== Question 1 ====

	Are the AMR genes found in the five genomes ?		Are the same AMR genes found in the five genomes ?

			==== Solution ====
			No

			</div>


	==== Question 2 ====		==== Question 2 ====
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	==== Solution ====		==== Solution ====
			No, three gene calls fails the criteria for a good match. Following command can be used the find the three gene calls:
	<pre>		<pre>
	~~fef~~		cat ~/microbial_exercise/output_abricate.txt \| cut -f1,6,10,11 \| awk '$3<=90 \|\| $4<=95'
	</pre>		</pre>

Rasmus: /* Task05: Detection of antimicrobial resistance genes */

2026-01-11T21:39:17Z

Task05: Detection of antimicrobial resistance genes

← Older revision		Revision as of 23:39, 11 January 2026
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	</pre>		</pre>

	Run Abricate on the ~~assembled genomes~~ using the Resfinder database:		Run Abricate on the five ST2326 genome assemblies using the Resfinder database:

	<pre>		<pre>
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	==== Question 1 ====		==== Question 1 ====

			Are the AMR genes found in the five genomes ?

	==== Question 2 ====		==== Question 2 ====

			Do all found AMR genes have a good match to a database reference gene ? (sequence coverage of > 90% and sequence identity > 95%)

	<div class="mw-collapsible mw-collapsed">		<div class="mw-collapsible mw-collapsed">

Rasmus: /* Task05: Detection of antimicrobial resistance genes */

2026-01-11T21:32:49Z

Task05: Detection of antimicrobial resistance genes

← Older revision		Revision as of 23:32, 11 January 2026
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	<pre>		<pre>
	abricate.sh --db resfinder /home/projects/microbial_genomics/task03_assemblies/ST2326*.fna		abricate.sh --db resfinder /home/projects/microbial_genomics/task03_assemblies/ST2326*.fna > ~/microbial_exercise/output_abricate.txt
	</pre>		</pre>

Rasmus: /* Task05: Detection of antimicrobial resistance genes */

2026-01-11T21:31:27Z

Task05: Detection of antimicrobial resistance genes

← Older revision		Revision as of 23:31, 11 January 2026
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	==== Question 2 ====		==== Question 2 ====

			<div class="mw-collapsible mw-collapsed">

			==== Solution ====
			<pre>
			fef
			</pre>

			</div>

	== Supplementary information and files ==		== Supplementary information and files ==

Rasmus at 21:30, 11 January 2026

2026-01-11T21:30:22Z

← Older revision		Revision as of 23:30, 11 January 2026
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	Your hospital have not yet implemented mNGS, but the hospital already uses NGS to sequence the genomes of bacterial isolates cultivated from clinical specimens. Accordingly, the hospital laboratory has sequenced the genome of a Stapholycoccus aureus isolate and have made 100,000 of the sequence reads available for you in <code>/home/projects/microbial_genomics/task01_sequence_reads/100K_cap_SH631x88_251212_LH00793_A22G7YYLT1_R1.fastq.gz</code>.		Your hospital have not yet implemented mNGS, but the hospital already uses NGS to sequence the genomes of bacterial isolates cultivated from clinical specimens. Accordingly, the hospital laboratory has sequenced the genome of a ''Stapholycoccus aureus'' isolate and have made 100,000 of the sequence reads available for you in <code>/home/projects/microbial_genomics/task01_sequence_reads/100K_cap_SH631x88_251212_LH00793_A22G7YYLT1_R1.fastq.gz</code>.

	The hospital laboratory asks you to run Kraken on the 100,000 reads with these commands:		The hospital laboratory asks you to run Kraken on the 100,000 reads with these commands:
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	</pre>		</pre>

	The vast majority of reads that could be classified to species-level are assigned to Stapholycoccus aureus, but also a minority of reads are assigned to other species.		The vast majority of reads that could be classified to species-level are assigned to ''Stapholycoccus aureus'', but also a minority of reads are assigned to other species.

	==== Question 4 ====		==== Question 4 ====