Oxford Nanopore scripts are considered confidential data. As such we release diffs to enable the recreation of the code used to control runs. 

Please note these scripts are only compatible with MinKNOW vs 1.3.25. Future updates to tuning scripts will be available through the Oxford Nanopore Community Forums.

These scrips are available in full on those forums at this time.

To recreate the tuning scripts for MinKNOW vs 1.3.25 please collect the following files from a windows installation of MinKNOW1.3.25.


Step 1. Collect source files.

Place the collected files into the appropriate folder in this collection.

From:

c:\grouper\binaries\ont-python\Lib\site-packages\bream\core\parameters\base_conditions

collect:

R9_base_condition_mux_scan.yml
R9_base_condition_mux_scan_MIN106.yml

From:

c:\grouper\binaries\ont-python\Lib\site-packages\bream\nc\parameters\experiment_conf

collect:

Sequencing_Run.yml
Sequencing_Run_MIN106.yml

From:

c:\grouper\binaries\ont-python\Lib\site-packages\bream\core\experiments

collect:

sequencing.py
mux_scan.py

From:

c:\grouper\binaries\python\recipes\nc

collect:

NC_48Hr_Sequening_Run_FLO-MIN106_SQK-LSK108.py
NC_48Hr_Sequening_Run_FLO-MIN106_SQK-RAD002.py

From:

c:\grouper\binaries\ont-python\Lib\site-packages\bream\nc\protocols

collect:

sequencing.py


Step 2. Apply the Patches

Each file must be patched and renamed as follows:


Patch R9_base_condition_mux_scan.yml with R9_base_condition_mux_scan.patch and rename patched file to R9_base_condition_mux_scan_tune.yml
Patch R9_base_condition_mux_scan_MIN106.yml with R9_base_condition_mux_scan_MIN106.yml and rename patched file to R9_base_condition_mux_scan_MIN106.yml

Patch Sequencing_Run.yml with Sequencing_Run.patch and rename to Sequencing_Run_tune.yml
Patch Sequencing_Run_MIN106.yml with Sequencing_Run_MIN106.patch and rename to Sequencing_Run_MIN106_tune.yml

Patch sequencing.py with sequencing.patch and rename to sequencing_tune.py
Patch mux_scan.py with mux_scan.patch and rename to mux_scan_tune.py

Patch NC_48Hr_Sequening_Run_FLO-MIN106_SQK-LSK108.py with NC_48Hr_Sequening_Run_FLO-MIN106_SQK-LSK108.patch and rename to NC_Tune_Sequening_Run_FLO-MIN106_SQK-LSK108.py
Patch NC_48Hr_Sequening_Run_FLO-MIN106_SQK-RAD002.py with NC_48Hr_Sequening_Run_FLO-MIN106_SQK-RAD002.patch and rename to NC_Tune_Sequening_Run_FLO-MIN106_SQK-RAD002.py

NB This step is different.

Copy sequencing.py and name it sequencing.bak

Patch sequencing.py with sequencing_tune.patch and rename to sequencing_tune.py

rename sequencing.bak to sequencing.py

Patch sequencing.py with sequencing_MIN106_tune.patch and rename to sequencing_MIN106_tune.py


After these patches are complete, the patched files need to be placed in the appropriate software folders as listed below:


Place files from the base_conditions folder into c:\grouper\binaries\ont-python\Lib\site-packages\bream\core\parameters\base_conditions

Place files from the experiment_conf folder into c:\grouper\binaries\ont-python\Lib\site-packages\bream\nc\parameters\experiment_conf

Place files from the experiments folder into c:\grouper\binaries\ont-python\Lib\site-packages\bream\core\experiments

Place files from the nc folder into c:\grouper\binaries\python\recipes\nc

Place files from the protocols folder into c:\grouper\binaries\ont-python\Lib\site-packages\bream\nc\protocols (This is the file where bias-voltage and repeats etc can be edited. Bias voltage changes should be in increments of-10mV and the flicking voltage should be incremented by the same number of -12mV steps)



Once this has been done you should be good to go and see script in the usual recipe window. Remember if you change the bias-voltage you need to change the flicking voltage accordingly as instructed above.

Note that these scripts only work with MinKNOW1.3.25