Basic Usage

Running Nomadic

Whenever you want to run Nomadic, first do the following:

• Make sure you have installed Nomadic from bioconda(see Installation).

• Open a terminal window and activate the Nomadic environment:

conda activate nomadic

• Navigate to your workspace (or location you want to create one - see next section)

cd path/to/your/workspace

Starting a workspace

Nomadic creates workspaces to help organise your input data and analysis results. A workspace is just a folder on your computer where all of the input data needed to run Nomadic, as well as your analysis results, are stored. You can create a workspace with the following command:

nomadic start pfalciparum

By default the name of the new workspace is nomadic. You can enter the workspace by typing:

cd nomadic

Inside the workspace, you should see the following folders:

Folder	Contents
beds	Contains information about amplicons used in sequencing.
metadata	Where you should put all of your metadata files.
results	Where the results from running Nomadic will go. Initially it will be empty.

Analysing a sequencing run in realtime

Nomadic can process nanopore squencing data being produced by MinKNOW in real-time. To do so, follow the steps below (steps 1 and 2 can be done in any order):

Step 1: Create a metadata file

Create a metadata file containing information about what barcodes you used in the sequencing library and their associated sample IDs. You can do this by manually entering values into a csv (comma separated value) file:

Only the barcode and sample_id columns are mandatory. The rest are optional, and you are also free to include any other columns you like.

Alternatively you can complete the Excel template ("NOMADS_Library_Worksheet.xlsx", stored in the metadata folder). The sheet guides a user through data entry including data validation checks and generates a experiment name that the file should be saved as. Post-PCR gel images can also be saved in this template for future reference.

The csv / excel file must be saved in the metadata folder of your workspace.

Step 2: Start nanopore sequencing with MinKNOW

Use MinKNOW to start nanopore sequencing. Ensure you give MinKNOW the exact experiment name you gave your metadata file.

Step 3: Start Nomadic

Launch Nomadic to start analysis, the dashboard will open in a browser window on your computer:

nomadic realtime <expt_name>

Viewing a completed experiment

Once an experiment is completed, you can still open the Nomadic dashboard to view your results by running:

nomadic dashboard <expt_name>