ont-guppy-duplex-pipeline 1.0.0

Oxford Nanopore Technologies duplex pipeline scripts for guppy

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/