Skip to content
Snippets Groups Projects
Select Git revision
  • master default protected
  • yguetlin-master-patch-20853
2 results
Blame Permalink
assembly_exercise.md 3.13 KiB

IMPORTANT If you have not done so before, please run the following command:

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 of 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

    # copy data 
cp -r /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/testdata/illumina/01_data /data/$USER/testdata/illumina/

# copy scripts
cp -r /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/testdata/illumina/02_scripts/ /data/$USER/testdata/illumina/

    Nanopore

    # copy data 
cp -r /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/testdata/nanopore/rawdata /data/$USER/testdata/nanopore/

# copy scripts
cp /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/testdata/nanopore/*.sh /data/$USER/testdata/nanopore/

    Hybrid

    # copy scripts
cp /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/testdata/hybrid/*.sh /data/$USER/testdata/hybrid/

Running the analysis

In the assembly scripts you need to specify the variables for the input and output data. Submit for each platform the respective assembly script.




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

    # copy data sets
cp -r /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/illumina/01_data_* /data/$USER/ngs/illumina/

# copy scripts
cp -r /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/illumina/02_scripts /data/$USER/ngs/illumina/

    Nanopore

    # copy data sets
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/

# copy all scripts
cp /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/nanopore_scripts/*.sh /data/$USER/ngs/nanopore/

    Hybrid

    # copy scripts
cp /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023//hybrid_assembly_scripts/*.sh /data/$USER/ngs/hybrid/

  • In the assembly scripts you need to specify the variables for the input and output data. Submit for each platform the respective assembly script.