Running raw read recovery - Linux, Mac, and Mk1C

(For raw read recovery on Windows 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 /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. Open up a terminal window

2. Navigate to the directory containing the recover_reads executable, by using the change directory command

cd

followed by therecover_reads executable location, usually in /opt/ont/minknow/bin for Linux and Mk1C users, and in /Applications/MinKNOW/bin for MacOS users. Newer MacOS users will find this located in /Applications/MinKNOW.app/Contents/Resources/bin/

An example command for Mk1C is as follows,
​minit@MC-100059:~$ cd /opt/ont/minknow/bin/

3. Run the following command to recover your raw reads:

./recover_reads "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:

./recover_reads /data/queued_reads/complete_reads_xxx --output-directory /data/../output

Reads will be recovered to the --output-directory specified.

These can then be basecalled using the post-run basecalling option in MinKNOW or stand-alone Dorado.