Data Transfer from the Mk1C Sequencing Device for Downstream Analysis

Once your MinION Mk1C sequencing run completes, these instructions detail how to transfer your reads from the machine to your computer using a flash drive, staging them for assembly and analysis with MIRA

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1. Plug your USB storage device into the side of the MK1C

2. On the MK1C screen, select File Manager and navigate into your runid

3. Navigate down to the “fastq_pass” folder and select the three dots to the right of it

4. Select copy, then you should be prompted to select “external drive”

5. Prepare your runfolder on your computer

• Prepare the ExperimentID folder
  • In files, navigate to Linux –> home –> [user] –> MIRA_NGS (Windows WSL) or FLU_SC2_SEQUENCING, depending on how you set up you MIRA installation
  • Inside of this folder, create a new folder with your RUN ID
    • Run IDs generally should contain the date sequenced and the pathogen

6. Move your fastq_pass folder from the USB drive into this RUNID folder

• You do NOT NEED to include the “unclassified” folder, since it is large and has unusable data

You now have staged yout Mk1C fastqs for analysis! You can proceed to Running MIRA