Rerio is comprised of "research release" basecalling models and configuration files.
The research models provide cutting-edge functions, speeds and accuracies that have not been productionised or validated by Oxford Nanopore Technologies. Nevertheless, models and config files can be run 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.
- 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)
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)
Follow the instructions below to use research models with Dorado executable. See further details for running Dorado here.
You will require:
- Python-compatible environment (e.g. Terminal)
- The most recent Dorado version, available on the Nanopore Community Software downloads page or the Dorado GitHub page.
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/dorado_models/[email protected]_url
| Config | DNA/RNA | Chemistry | Device | Tested Dorado | Notes |
|---|---|---|---|---|---|
| res_dna_r10.4.1_e8.2_400bps_sup@2023-09-22_bacterial-methylation | DNA | R10.4.1 E8.2 | All | v0.3.4 | Kit 14 5kHz Research model with an increased range of bacterial methylation motifs |
| [email protected] | DNA | R10.4.1 E8.2 | All | v0.3.0 | Kit 14 4kHz Model Compatible with All-context Modified Bases |
| [email protected]_5mC@v2 | DNA | R10.4.1 E8.2 | All | v0.3.0 | Kit 14 4kHz 5mC All-context Modified Base Model |
| [email protected]_6mA@v2 | DNA | R10.4.1 E8.2 | All | v0.3.0 | Kit 14 4kHz 6mA All-context Modified Base Model |
| [email protected]_4mC_5mC@v1 | DNA | R10.4.1 E8.2 | All | v0.4.3 | Kit 14 5kHz 4mC+5mC All-context Modified Base Model |
# Download all models python3 download_model.py --dorado # Download particular model python3 download_model.py --dorado dorado_models/[email protected]_4mC_5mC@v1_url
Each model will be downloaded to dorado_models/{config}.
Basecalling models can be supplied directly to Dorado. Please refer to the Dorado README for more information on how to run basecalling and use modified base models.
Clair3 models for the following configurations are available:
Latest:
| Config | Chemistry | Dorado basecaller model |
|---|---|---|
| r1041_e82_400bps_sup_v500 | R10.4.1 E8.2 (5kHz) | v5.0.0 SUP |
| r1041_e82_400bps_hac_v500 | R10.4.1 E8.2 (5kHz) | v5.0.0 HAC |
| r1041_e82_400bps_sup_v410 | R10.4.1 E8.2 (4kHz) | v4.1.0 SUP |
| r1041_e82_400bps_hac_v410 | R10.4.1 E8.2 (4kHz) | v4.1.0 HAC |
Deprecated:
| Config | Chemistry | Dorado basecaller model | Guppy basecaller |
|---|---|---|---|
| r1041_e82_400bps_sup_v430 | R10.4.1 E8.2 (5kHz) | v4.3.0 SUP | |
| r1041_e82_400bps_hac_v430 | R10.4.1 E8.2 (5kHz) | v4.3.0 HAC | |
| r1041_e82_400bps_sup_v420 | R10.4.1 E8.2 (5kHz) | v4.2.0 SUP | |
| r1041_e82_400bps_hac_v420 | R10.4.1 E8.2 (5kHz) | v4.2.0 HAC | |
| r1041_e82_260bps_sup_v400 | R10.4.1 E8.2 | v4.0.0 SUP | |
| r1041_e82_260bps_hac_v400 | R10.4.1 E8.2 | v4.0.0 HAC | |
| r1041_e82_260bps_fast_g632 | R10.4.1 E8.2 | v3.5.2 FAST | v6.3.2 FAST |
| r1041_e82_400bps_sup_g615 | R10.4.1 E8.2 | v3.5.2 SUP | v6.1.5 SUP |
| r1041_e82_400bps_hac_g632 | R10.4.1 E8.2 | v3.5.2 HAC | v6.3.2 HAC |
| r1041_e82_400bps_hac_g615 | R10.4.1 E8.2 | v6.1.5 HAC | |
| r1041_e82_400bps_fast_g615 | R10.4.1 E8.2 | v6.1.5 FAST | |
| r1041_e82_260bps_sup_g632 | R10.4.1 E8.2 | v3.5.2 SUP | v6.3.2 SUP |
| r1041_e82_260bps_hac_g632 | R10.4.1 E8.2 | v3.5.2 HAC | v6.3.2 HAC |
| r1041_e82_400bps_fast_g632 | R10.4.1 E8.2 | v3.5.2 FAST | |
| r104_e81_sup_g5015 | R10.4 E8.1 | v5.0.15 SUP | |
| r104_e81_hac_g5015 | R10.4 E8.1 | v5.0.15 HAC |
# 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}.
Most Remora models are supplied along with the Remora repository, but models with less validation intended for research purposes will be released in Rerio.
| Config | DNA/RNA | Pore | Device | Tested Guppy | Notes |
|---|---|---|---|---|---|
| 5mC_all_context_sup_r1041_e82 | DNA | R10.4.1 | Any | v6.1.2 | 5mC in all context (with SUP basecaller) |
# 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}.pt (or remora_models/{config}.onnx for Remora version <2.0).
These models can be supplied directly to Bonito via the --modified-base-model argument.
This section contains research release Guppy compatible models. See Nanopore Community page for download/install instructions. Since research models often utilise new features, the latest version of Guppy may be required.
| Config | DNA/RNA | Pore | Device | Tested Guppy | Notes |
|---|---|---|---|---|---|
| res_dna_r9.4.1_e8.1_{fast,hac,sup}_v033.cfg | DNA | R9.4.1 | All | v5.0.11 | Kit 12 E8.1 CRF Models |
| res_dna_r941_min_crf_v032.cfg | DNA | R9.4.1 | MinION/GridION | v4.4.0 | Bonito CRF |
| res_dna_r103_min_crf_v032.cfg | DNA | R10.3 | MinION/GridION | v4.4.0 | Bonito CRF |
| res_dna_r103_q20ea_crf_v033.cfg | DNA | R10.3 | PromethION | v5.0.11 | Q20 early access CRF |
| res_dna_r103_q20ea_crf_v034.cfg | DNA | R10.3 | PromethION | v5.0.11 | Q20 early access CRF |
| res_dna_r941_min_flipflop_v001.cfg | DNA | R9.4.1 | MinION/GridION | v3.5.1 | |
| res_dna_r941_min_dUfast_v001.cfg | DNA | R9.4.1 | MinION/GridION | v3.5.1 | Calls dU as dT (fast) |
| res_dna_r941_min_dUhac_v001.cfg | DNA | R9.4.1 | MinION/GridION | v3.5.1 | Calls dU as dT (high acc.) |
| res_dna_r941_min_rle_v001.cfg | DNA | R9.4.1 | MinION/GridION | v3.5.1 | |
| res_dna_r103_min_flipflop_v001.cfg | DNA | R10.3 | MinION/GridION | v3.5.1 | |
| res_dna_r103_prom_rle_v001.cfg | DNA | R10.3 | PromethION | v3.5.1 | |
| res_rna2_r941_min_flipflop_v001.cfg | RNA2 | R9.4.1 | MinION/GridION | v3.5.1 |
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 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
© 2020-2023 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:https://nanoporetech.com
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.
