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exercises/assembly_exercise.md

+## **IMPORTANT** If you have not done so before, please run the following command:
+
+```bash
+echo "export SINGULARITY_BINDPATH=/scratch,/data,/home/$USER,/shares/amr.imm.uzh" >> $HOME/.bashrc
+source $HOME/.bashrc
+```
+
+
+We will first do the assembly of a small test dataset together. Later, you will run the same analysis on all samples of the two projects (MRSA and UPEC). 
+
+
+## Assembly on test dataset
+
+### Preparation 
+
+* In your `data` space (that is `/data/$USER`), please create a directory called `testdata` Inside `testdata`, make a directory for each assembly approach, i.e. `nanopore`, `illumina`, `hybrid`. 
+
+
+* Copy the following datasets
+
+   **Illumina**
+
+
+    ```bash
+    cp -r /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/testdata/illumina/01_data /data/$USER/testdata/illumina/
+
+    cp -r /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/illumina/testdata/02_scripts/ /data/$USER/testdata/illumina/
+    ```
+
+    
+    **Nanopore**
+
+    ```bash
+    cp -r /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/testdata/nanopore/rawdata /data/$USER/testdata/nanopore/
+
+    cp /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/testdata/nanopore/rawdata/WGS_nanopore_assembly_mrsa.sh /data/$USER/testdata/nanopore/
+    ```
+
+
+
+    **Hybrid**
+
+    ```bash
+    cp /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/testdata/hybrid/hybrid_assembly_mrsa.sh /data/$USER/testdata/hybrid/
+    ```
+
+
+
+
+### Running the analysis
+
+In the assembly scripts you need to specify the `datadir` variables. 
+Submit for each platform the respective assembly script. 
+
+
+
+<br><br><br>
+
+## Assembly of project dataset
+
+* In your `data` space, please create a directory called `ngs`. Inside `ngs`, make a directory for each assembly approach, i.e. `nanopore`, `illumina`, `hybrid`. 
+
+* Copy the following datasets
+    
+    **Illumina**
+
+    ```bash
+    cp -r /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/illumina/01_data_* /data/$USER/ngs/illumina/
+
+    cp -r /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/illumina/02_scripts /data/$USER/ngs/illumina/
+    ```
+
+    **Nanopore**
+
+    ```bash
+    cp -r /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/nanopore/Group1_mrsa/rawdata_mrsa /data/$USER/ngs/nanopore/
+
+    cp -r /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/nanopore/Group2_upec/rawdata_upec /data/$USER/ngs/nanopore/
+
+    cp /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/nanopore_scripts/WGS_nanopore_assembly* /data/$USER/ngs/nanopore/
+    ```
+
+    **Hybrid**
+
+    ```bash
+    cp /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023//hybrid_assembly_scripts/hybrid_assembly_* /data/$USER/ngs/hybrid/
+    ```
+
+* In the assembly scripts you need to specify the `datadir` variables. 
+Submit for each platform the respective assembly script. 
+    
+
+
+
+
+
+