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MIRA is an interactive dashboard created using Dash, a python framework written on the top of Flask, Plotly.js and React.js. The dashboard allows users to interactively create a metadata and config file for running Influenza Genome and SARS-CoV-2 Spike-Gene Assembly. Coming soon, it will allow for upload via FTP to NCBI’s databases Genbank, BioSample, and SRA, as well as GISAID.
MIRA’s dashboard relies on four Docker containers to run its genome assembly and curation:
Need to set up an Ubuntu OS? Follow instructions in Getting Started.
sudo apt-get update
sudo apt-get install ca-certificates curl gnupg lsb-release
Enter
sudo mkdir -p /etc/apt/keyrings
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /etc/apt/keyrings/docker.gpg
echo "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
sudo apt-get update
sudo chmod a+r /etc/apt/keyrings/docker.gpg
sudo apt-get update
sudo apt-get install docker-ce docker-ce-cli containerd.io docker-compose-plugin
sudo docker run hello-world
FLU_SC2_SEQUENCING
to save your sequencing reads to. From the command line, run: mkdir ~/FLU_SC2_SEQUENCING
cd ~/FLU_SC2_SEQUENCING
curl https://raw.githubusercontent.com/CDCgov/MIRA/prod/docker-compose-git.yml | sed "s%/path/to/data%$(pwd)/%g" > docker-compose.yml
sudo docker compose up -d
Click here to download tiny test data from ONT Influenza genome and SARS-CoV-2-spike - 40Mb
unzip the file and find two folders:
tiny_test_run_flu
tiny_test_run_sc2
move these folders into FLU_SC2_SEQUENCING
Open your browser and type http://localhost:8020 in the address bar.
Click Refresh Run Listing
in MIRA, you should now see these folders listed.
Click Download Samplesheet
.
Save the samplesheet and then upload it by clicking on Drag and Drop your Samplesheet or Click and Select the File
In the dropdown box 'What kind of data is this?', select the correct data type.
Click 'START GENOME ASSEMBLY'
Toggle 'Watch IRMA progress' to see IRMA's stdout stream.
When "IRMA is finished!" is displayed, Click "DISPLAY IRMA RESULTS"