2026 Level 2 proficiency testing¶

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Exercises: 150 minutes

Key information

The aim is to complete each of the exercises before the end of the session.
This testing is open book - you may use any materials from the level 2 training and anything online.
This testing is individual - please do not discuss your solutions with other trainees.
The tutors are here to help with significant technical issues such as loss of connection. We are not here to help you identify tools or how to solve specific questions.

All test folders are located in the following location:

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~/level2_proficiency/

Output files

For each exercise, you are free to name your output folders/files whatever you wish.

Please ensure that your results are in the appropriate folder for each exercise, however.

Reporting findings

Whenever an exercise asks your to in some way interpret an output file and report your results, just create a small text file to store your notes.

Name the file according to the exercise that asked for the information.

Exercise 1¶

Navigate to your instance of the 01_assembly/ folder. You have been provided with the following files:

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reads/illumina_R1.fq.gz
reads/illumina_R2.fq.gz
reads/nanopore.fq.gz
reference/reference.fna
results/provided_illumina.fna
results/provided_nanopore.fna

Part 1

Create a draft genome assembly from the Illumina sequences from the reads/ folder using an appropriate assembly tool.

This job will take about 10 minutes to complete with 4 CPUs.

Part 2

Create a draft genome assembly from the Oxford Nanopore sequences from the reads/ folder using an appropriate assembly tool.

This job will take about 5 minutes to complete.

Part 3

Use an appropriate tool to determine assembly statistics for your two assemblies file, using the file reference/reference.fna as your reference genome.

If your assemblies do not complete in a reasonable amount of time, you can use the results/provided_illumina.fna results/provided_nanopore.fna file instead of your own output.

Report the folllowing metrics for each assembly:

Number of contigs with length greater than or equal than 50 kbp.
The number of misassemblies, and the misassembled contig length.
Fraction of the reference genome covered in the assemblies.

Exercise 2¶

Navigate to your instance of the 02_polish/ folder. You have been provided with the following file:

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resources/draft_asm.fna
resources/reads.fq.gz
reference/reference.fna

Part 1

Perform a round of polishing on the draft_asm.fna genome file using the reads available.

Part 2

Use an appropriate tool to determine assembly statistics for the original assembly file and your revised versions using the file reference/reference.fna as your reference genome. Provide a quick comment (one sentence) on whether or not polishing improved the assembly based upon the mismatches and indel counts.

Exercise 3¶

Navigate to your instance of the 03_mapping/ folder. You have been provided with the following files:

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reads/nanopore.fq.gz
reference/reference.fna
results/provided_mapping.sam

Part 1

Use whatever tool is appropriate to map the sequences in the reads/ folder against the reference file, creating a sam file with the mapping results.

Part 2

Once you have completed mapping your reads, sort and compress the mapping information from your output sam file.

If you are unable to complete your mapping job for any reason, use the file supplied at `results/provided_mapping.sam.

Produce a depth report from the compressed mapping file.
When you have produced your compressed file, filter the results to keep only the mapped reads in the mapping output.

Exercise 4¶

Navigate to your instance of the 04_classification_kraken2/ folder. You have been provided with the following files:

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inputs/input_sequences.fna
results/provided_kraken2.txt

Part 1

Run the kraken2 classification of the sequences provided in inputs/input_sequences.fna.

When selecting a database, use the PlusPFP database located at:

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~/level2/databases/k2_pluspfp/

Check your notes carefully to make sure you understand how to direct kraken2 towards this database.

Part 2

You have been provided with an output file of the above classification job - results/provided_kraken2.txt. Use your knowledge of the command line to search through the output file and identify the most likely species to be in this sample.

Create a text file containing your findings. You do not need to report every species hit in the provided_kraken2.txt file - just pick the candidates you believe are most likely and give a quick 1-sentence justification for each choice.

Exercise 5¶

Navigate to your instance of the 05_classification_diamond/ folder. You have been provided with the following file:

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inputs/input_sequences.faa
reference/uniprot_sprot.tax
results/provided_diamond.txt

Part 1

Run the diamond classification tool on the sequences provided in inputs/input_sequences.faa.

When selecting a database, use the uniprot_sprot.dmnd database located at:

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~/level2/databases/swissprot_dmnd/uniprot_sprot.dmnd

Part 2

Examine the outputs of the file results/provided_diamond.txt, remembering the BLAST6 format for column meaning.

Based on the top hit results, identify which target(s) you believe are most probable for each query sequence. You can find taxonomic information for each target sequence in the reference/uniprot_sprot.tax file. Use the target sequence name to find the most likely genus or species of the organism from which these sequences were obtained. Create a text file containing your conclusion.

Selective reporting

When looking up classification information in the uniprot_sprot.tax file you do not need to report every hit for each query. Use your judgement for which targets are most likely for each query, and just report these.

Closing out the test¶

When you have completed all of the exercises, and you are happy with your results, please run the following command to log the history of your command line to a file.

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history > ~/level2_proficiency/history_log.txt