Running raw read recovery - WINDOWS

(For raw read recovery on Mac, Linux, and Mk1C please see here).

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 stand-alone Guppy.