A work in progress.
An installable environment and code for the Jetson Xaiver to analyse clinical bacterial isoaltes from nanopore sequencing data. This is a baseline minimum viable versions without the proposed results dashboard and other features.
This analysis pipeline is designed to make read classificaion easy to run at a point-of-care setting. It will also produce some simple sequence data QC plots for each sample included in the run. The only expeced input for the programe is a barcoded ONT sequence run output directory. The program will search through the output directory to find each barcode and treat each one as a sample. Results will be printed to the screen and saved to a results directory too.
Requires conda to be installed on the system already. It uses conda to add a small number of pretty standard python packages (see environment.yml). These will, and can be, installed in the base conda environment, or which ever environment is activated at the time of install. As it is expected this is a dedicated sequencing device, the base conda environment will be the easiest for the end user. For future updates a dedicated environment my be used.
To install:
- clone the git repo:
git clone https://github.com/ESR-NZ/POx_POC_pipeline.git - move into the downloaded repo:
cd POx_POC_pipeline - run the install script:
./install_pipeline.sh - Enter the path to the mounted SSD on the system when prompted.
The above commands will download and build the other software dependencies needed to run the analysis; namely seqkit and kraken2. Acknowledgements to the authors of this excellent software.
The first time the install script (install_pipeline.sh) is run it will also download the required kraken2 database to the SSD.
You will need to add the created bin directory to your path, as well as, an environent variable (KRAKEN2_DB_PATH) so the run script knows where to find the kraken2 database. There are instructions to copy/paste the required lines to your .bascrc file shown at the end of the install process, so watch out for those.
Once installed, the "pipeline" can be run with the command:
POX-POC_run.py <path/to/run_directory>
Results can be found in:
path/to/run_directory/POx_POC_results
This can be run during the sequencing experiment if required to analyse the data generated upto that point.
to write...