Metadata-Version: 2.1
Name: ont-guppy-duplex-pipeline
Version: 1.0.1
Summary: Oxford Nanopore Technologies duplex pipeline scripts for guppy
Home-page: https://nanoporetech.com
Author: Oxford Nanopore Technologies plc
License: MPL 2.0
Keywords: guppy duplex basecalling nanopore
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)
Classifier: Natural Language :: English
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Requires-Dist: parasail
Requires-Dist: pandas
Requires-Dist: pyfastx

ont_guppy_duplex_pipeline
=========================

``ont_guppy_duplex_pipeline`` is a tool to process duplex data
contained in .fast5 files.

.. note::

   ont_guppy_duplex_pipeline *only* works on r10.4 e8.1 data.

The duplex pipeline comprises the following steps:

1. (Optional) simplex (1d) basecalling using the fast model.
2. Identification of duplex pairs in the simplex basecall results.
3. (Optional) duplex basecalling of those pairs.
4. (Optional) simplex basecalling of all reads that were not part of a
   duplex pair, using the sup model.

Getting Started
===============

``ont_guppy_duplex_pipeline`` is available on PyPI and can be installed via pip:::

    pip install ont-guppy-duplex-pipeline

Launch the pipeline by calling ``guppy_duplex``:::

    guppy_duplex -i <read folder> -s <output_folder>

See the full list of arguments by looking at the help for ``guppy_duplex``:::

    guppy_duplex -h

Find out more about guppy and duplex on the Oxford Nanopore
Technologies community: https://community.nanoporetech.com/


