nanoporetech / rerio

Rerio

Rerio is comprised of "research release" basecalling models and configuration files. All basecalling models are compatible with Guppy (see Nanopore Community page for download/install instructions). Since research models often utilise new features, the latest version of Guppy may be required.

The research models provide cutting-edge functions, speeds and accuracies that have not been productionised or validated by Oxford Nanopore Technologies in the Guppy executable basecaller. Nevertheless, models and config files can be run with the basecalling infrastructure in Guppy executable by using the instructions available in this repository.

Models are provided for DNA and RNA, various pore types and to basecall different modified bases in a variety of contexts.

Additionally, Rerio hosts research models for the short variant caller Clair3.

Features

• New and advanced research models that are at the forefront of nanopore sequencing analyses (e.g. highest accuracies, quickest speeds, more modified basecalls in more contexts)
• Functions with Megalodon (2.0 and above) to call modified DNA bases

Note: The results generated by research basecalling models have not been scrutinized nor validated and Oxford Nanopore cannot support each use case (see Research Release disclaimer)

Getting started

Follow the instructions below to use research models with Guppy executable. See further details for running Guppy here.

Dependencies

You will require:

• Python-compatible environment (e.g. Terminal)
• The most recent Guppy version, available on the Nanopore Community Software downloads page.

Note: Rerio is versioned by the minimum version of Guppy required to run _all_ models in the repository. A new release of Rerio will be tagged when a model is added that requires a more recent version of Guppy.

Installation

Rerio can be downloaded by cloning from GitHub git clone https://github.com/nanoporetech/rerio. Once Rerio has been downloaded, models can be downloaded via the download_model.py script.

# Download all models
rerio/download_model.py
# Download specific model(s)
rerio/download_model.py rerio/basecall_models/res_dna_r9.4.1_e8.1_sup_v033.cfg

Once desired models have been downloaded, they can be run by specifying the Guppy data path option (-d or --data_path) and selecting the desired config file (-c or --config).

./ont-guppy/bin/guppy_basecaller -i fast5s/ -s basecalled_fast5s \
   -d ./rerio/basecall_models/ \
   -c res_dna_r9.4.1_e8.1_sup_v033.cfg

Use and description of basecaller models

Megalodon Support

Rerio research models can be run within megalodon by specifying the data directory in the --guppy-params argument.

megalodon fast5s/ --guppy-params "-d ./rerio/basecall_models/" \
    --guppy-config res_dna_r9.4.1_e8.1_sup_v033.cfg

Barcoding Support

The Rerio GitHub code repository includes a minimal barcoding stub to allow Guppy to run successfully. In order to enable full Guppy barcoding capabilities, all barcoding files must be transferred from the guppy data directory to the rerio data directory.

cp ont-guppy/data/barcoding/* rerio/basecall_models/barcoding/

Taiyaki Models

Taiyaki checkpoint files corresponding to Rerio research models are provided. Not all of these are compatible with the public release of Taiyaki.

#  Download all models
python3 download_models.py --checkpoints
#  Download particular model
python3 download_models.py --checkpoints taiyaki_checkpoint/model

Clair3 Models

Clair3 models for the following configurations are available:

Latest:

Deprecated:

#  Download all models
python3 download_model.py --clair3
#  Download particular model
python3 download_model.py --clair3 clair3_models/{config}_model

Each model will be downloaded to the folder clair3_models/{config}.

Remora Models

Most Remora models are supplied along with the Remora repository, but models with less validation intended for research purposes will be released in Rerio.

#  Download all models
python3 download_model.py --remora
#  Download particular model
python3 download_model.py --remora remora_models/5mC_all_context_sup_r1041_e82

Each model will be downloaded to remora_models/{config}.onnx.

These models can be supplied directly to Bonito via the --modified-base-model argument and to Megalodon via the --remora-model argument.

Help

Licence and Copyright

© 2020, 2021 Oxford Nanopore Technologies Ltd.

Rerio is distributed under the terms of the Oxford Nanopore Technologies, Ltd. Public License, v. 1.0. If a copy of the License was not distributed with this file, You can obtain one at http://nanoporetech.com

Research Release

Research releases are provided as technology demonstrators to provide early access to features or stimulate Community development of tools. Support for this software will be minimal and is only provided directly by the developers. Feature requests, improvements, and discussions are welcome and can be implemented by forking and pull requests. However much as we would like to rectify every issue and piece of feedback users may have, the developers may have limited resource for support of this software. Research releases may be unstable and subject to rapid iteration by Oxford Nanopore Technologies.