ont_guppy_duplex_pipeline

ont_guppy_duplex_pipeline is a tool to process duplex data contained in .fast5 and/or .pod5 files.

The duplex pipeline comprises the following steps:

1. (Optional) simplex (1d) basecalling. This defaults to using dna_r10.4.1_e8.2_400bps_fast.cfg as the configuration.

2. Identification of duplex pairs in the simplex basecall results.

3. (Optional) duplex basecalling of those pairs. This defaults to using dna_r10.4.1_e8.2_400bps_sup.cfg as the configuration.

4. (Optional) simplex basecalling of all reads that were not part of a duplex pair, using the same configuration as the duplex basecalling.

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>

By default the pipeline is configured for the 10.4.1 e8.2 chemistry at 400bps. This can be changed by setting the --simplex_config and --duplex_config options. For example, to use the 260bps configurations::

guppy_duplex -i <read folder> -s <output_folder> --simplex_config dna_r10.4.1_e_8.2_260bps_fast.cfg --duplex_config dna_r10.4.1_e8.2_260bps_sup.cfg

Typically the simplex config should be a fast model and the duplex config should be a sup model.

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/