If MinKNOW™ ends a run without clearing up correctly, e.g. due to MinKNOW crash or unexpected computer shutdown, raw read data can be left in the C:\data\queued_reads\complete_reads_xxxx directory without being converted to pod5 files.

These raw data files can be converted into .pod5 files using a command line tool that is packaged within the MinKNOW suite: 1. Navigate to the directory containing the recover_reads executable, usually present at this location - C:\Program Files\OxfordNanopore\MinKNOW\bin 2. This directory should contain the binary file: recover_reads 3. Open up a terminal window by clicking on the search bar, typing in “Command prompt”, then right-clicking on “Run as administrator”. 4. Run the command below: cd C:\Program Files\OxfordNanopore\MinKNOW\bin 5. Run the following command to recover your raw reads: recover_reads.exe "location of your raw reads" --output-directory "location to output your recovered pod5s"

Please Note: The complete_reads_xxx folder should be the one generated during the time of the sequencing run that ended improperly An example command is shown below:

C:\Program Files\OxfordNanopore\MinKNOW\bin>recover_reads.exe C:\data\queued_reads\complete_reads_xxx --output-directory C:\..\output

Reads will be recovered to the--output-directory specified. These can then be basecalled using MinKNOW post-run basecalling or Dorado.