-
Command prompt:
Launch a terminal on your system. For example, when using Ubuntu, you can type Ctrl + Alt + T. You will run 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:
-
guppy_basecaller
(or the fully-qualified path if using the archive installer) -
--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:
-
--config
configuration file containing Guppy parameters
or
-
--flowcell
flow cell version--kit
sequencing kit version
-
-
Additional options can be specified to enable different basecalling features and output formats and these are discussed further in later sections.
Note that on Linux-based platforms it is also possible to pipe files into Guppy, as follows:
ls input_folder/*.fast5 | guppy_basecaller --save_path output_folder/basecall --config dna_r9.4.1_450bps_fast.cfg
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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:
guppy_basecaller -h
or
guppy_basecaller --help
To call out a list of available flow cells plus kit combinations, and their associated config files, use the command:
guppy_basecaller --print_workflows
Or if the model versions are not required, for faster display use:
guppy_basecaller --print_workflows --skip_model_versions
The command
-–version
shows the version of Guppy that is installed.