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docs/level2/51_proficiency.md

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+# 5.1 - Level 2 proficiency testing
+
+!!! clock "time"
+
+    * Exercises: 150 minutes
+
+!!! circle-info "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 1 or 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:
+
+    !!! terminal "code"
+
+        ```bash
+        /nesi/project/nesi03181/phel/proficiency/USERNAME/
+        ```
+
+!!! warning "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.
+
+!!! warning "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_illumina_assembly/` folder. You have been provided with the following files:
+
+!!! terminal "code"
+
+    ```
+    reads/illumina_R1.fq.gz
+    reads/illumina_R2.fq.gz
+    reference/reference.fna
+    results/provided_assembly.fna
+    ```
+
+!!! question "Part 1"
+
+    You are to produce a `slurm` script that uses an approriate assembly tool to assemble the Illumina MiSeq sequences in the `reads/` folder into a draft genome.
+
+    >Your script will only need about 10 minutes to complete with 16 CPUs.
+
+!!! question "Part 2"
+
+    Use an appropriate tool to determine assembly statistics for your assembly file and use the file `reference/reference.fna` as your reference genome.
+
+    >If your job does not complete in a reasonable amount of time, you can use the provided `results/provided_assembly.fna` file instead of your own output.
+
+    Report the folllowing metrics from your assembly:
+
+    1. Number of contigs with length greater than or equal than 50 kbp.
+    1. The N50 value for the assembly.
+    1. Number of indels relative to the reference genome.
+
+---
+
+## Exercise 2
+
+Navigate to your instance of the `02_mapping/` folder. You have been provided with the following files:
+
+!!! terminal "code"
+
+    ```
+    reads/nanopore.fq.gz
+    reference/reference.fna
+    results/provided_mapping.sam
+    ```
+
+!!! question "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.
+
+!!! question "Part 2"
+
+    1. 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.
+
+    2. Produce a depth report from the compressed mapping file.
+
+    3. When you have produced your compressed file, filter the results to keep only the **mapped** reads in the mapping output.
+
+---
+
+## Exercise 3
+
+Navigate to your instance of the `03_gene_calling/` folder. You have been provided with the following file:
+
+!!! terminal "code"
+
+    ```
+    input_sequences.fna
+    ```
+
+!!! question "Question"
+
+    You have been provided with a draft assembly of a prokaryotic genome. Create predictions of the protein coding regions of the assembly using whichever tool you believe is appropriate.
+
+---
+
+## Exercise 4
+
+Navigate to your instance of the `04_classification_kraken2/` folder. You have been provided with the following files:
+
+!!! terminal "code"
+
+    ```
+    inputs/input_sequences.fna
+    results/provided_kraken2.txt
+    ```
+
+!!! question "Part 1"
+
+    Write a `slurm` script to execute a `kraken2` classification of the sequences provided in `inputs/input_sequences.fna`.
+
+    When selecting a database, use the `PlusPFP` database located at:
+
+    !!! terminal "code"
+
+        ```
+        /nesi/project/nesi03181/phel/databases/k2_pluspfp_16gb_20231009/
+        ```
+
+    Check your notes carefully to make sure you understand how to direct `kraken2` towards this database.
+
+!!! question "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:
+
+!!! terminal "code"
+
+    ```
+    inputs/input_sequences.faa
+    results/provided_diamond.txt
+    ```
+
+!!! question "Part 1"
+
+    Write a `slurm` script to execute a `diamond` classification of the sequences provided in `inputs/input_sequences.faa`.
+
+    When selecting a database, use the `uniprot_sprot.dmnd` database located at:
+
+    !!! terminal "code"
+
+        ```
+        /nesi/project/nesi03181/phel/databases/swissprot_dmnd/uniprot_sprot.dmnd
+        ```
+
+!!! question "Part 2"
+
+    Examine the outputs of the file `results/provided_diamond.txt`, remembering the [BLAST6 format](https://genomicsaotearoa.github.io/hts_workshop_mpi/level2/44_annotation_protein/#comparing-the-outputs) for column meaning.
+
+    Based on the top hit results, determine the most likely genus or species of the organism from which these sequences were obtained. Create a text file containing your conclusion.
+
+---
+
+
+## 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.
+
+!!! terminal "code"
+
+    ```bash
+    history > /nesi/project/nesi03181/phel/proficiency/USERNAME/history_log.txt
+    ```
+
+---