Quickstart for the impatient

If you know how to install python packages from PyPI and how to use the command line, you can follow the instructions in this section to get PacBio Data Processing up and running.

Alternatively, if you need a step-by-step guide to use PacBio Data Processing on a cluster, follow the Quickstart on a cluster guide.

Installation

To install PacBio Data Processing, open an interactive shell and run:

pip install PacBioDataProcessing

or, alternatively:

python -m pip install PacBioDataProcessing

And that’s it!

On sm-analysis-gui

By default pip install PacBioDataProcessing does not enable the GUI program sm-analysis-gui. This program is considered an extra feature, since its usage depends on the wxpython library, whose installation must be done independently.

Note

More details as well as alternative installation methods are explained in Installation.

Warning

Although the installation of PacBio Data Processing is now complete, there are some runtime dependencies, which means that the dependencies must be there before using PacBio Data Processing. See Other dependencies and the links therein for the list of dependencies and suggestions on how to install them.

Using PacBio Data Processing

Once PacBio Data Processing and its dependencies have been installed, the sm-analysis executable can be used to perform a single molecule analysis of m6A methylations in DNA. For that you need:

• a BAM file with the results of the sequencing, and

• the reference file: a .fa/.fasta (the companion .fa.fai/.fasta.fai file will be generated if missing)

and feed the sm-analysis program with those files.

For example, if the bam file’s name is mysequence.bam and the reference file is called myreference.fasta, then the sm-analysis program will carry out a single molecule analysis of the m6A methylations found during sequencing with the following command:

sm-analysis mysequence.bam myreference.fasta

What’s next?

In the Single molecule analysis with the sm-analysis program section of the documentation you can find detailed information about the output that you can expect from sm-analysis and the possible input options available to customize its behaviour.

Check the Usage section to learn more about how to use PacBio Data Processing. Or have a look at the Guides section for more advanced/specific documentation on selected topics.