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Command prompt
Launch a command prompt. To do this, click on Start and type "Command prompt" in the search box, then click the link. You will be running all Guppy operations from here:
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Required parameters
To start a sequencing run with Guppy, you will need to type a command that specifies, as a minimum, the following parameters:
- The configuration file to use*
- The full path to the directory where the raw read files are located
- The full path to the directory where the basecalled files will be saved
* Rather than explicitly specifying a configuration file, Guppy can automatically select the appropriate configuration when the user specifies the flow cell and kit that have been used for the experiment.
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Default parameters
If you only specify the parameters listed above, Guppy will run with a number of other parameters set at their default values, for example:
- Q-score filtering will be set to ON
- File compression will be set to OFF
- Sequence reversal and U to T substitution for RNA will be set to OFF
For a full list of all the optional parameters and their default values, refer to the “Setting up a run: configurations and parameters” section of the protocol.
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Command-line entries for basecalling
To basecall reads with Guppy, you will need to use the following commands:
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"C:\Program Files\OxfordNanopore\ont-guppy-cpu\bin\guppy_basecaller.exe"
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--input_path
Full or relative path to the directory where the raw read files are located. The folder can be absolute (e.g.C:\data\my\_reads
) or a relative path to the current working directory (e.g...\my\_reads
) -
--save_path
Full or relative path to the directory where the basecall results will be saved. The folder can be absolute or a relative path to the current working directory. This folder will be created if it does not exist using the path you provide. (e.g. if it is a relative path, it will be relative to the current working directory)
Then either:
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--config
configuration file containing Guppy parameters
or
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--flowcell
flow cell version--kit
sequencing kit version
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General help command-line options:
For general help, the following available command-line options,
-h
or--help
, are provided within the Guppy toolkit:
"C:\Program Files\OxfordNanopore\ont-guppy-cpu\bin\guppy_basecaller.exe" -h
or
"C:\Program Files\OxfordNanopore\ont-guppy-cpu\bin\guppy_basecaller.exe" --help
To call out a list of available flow cells plus kit combinations, and their associated config files, use the command:
"C:\Program Files\OxfordNanopore\ont-guppy-cpu\bin\guppy_basecaller.exe" --print_workflows
The command
-–version
shows the version of Guppy that is installed.