https://github.com/nanoporetech/rerio
Research release basecalling models and configurations
https://github.com/nanoporetech/rerio
basecalling nanopore
Last synced: about 1 month ago
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Research release basecalling models and configurations
- Host: GitHub
- URL: https://github.com/nanoporetech/rerio
- Owner: nanoporetech
- License: other
- Created: 2020-03-18T09:05:35.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2024-06-18T20:48:01.000Z (over 1 year ago)
- Last Synced: 2025-04-06T08:02:15.697Z (6 months ago)
- Topics: basecalling, nanopore
- Language: Python
- Homepage: https://nanoporetech.com/
- Size: 119 KB
- Stars: 108
- Watchers: 33
- Forks: 10
- Open Issues: 4
-
Metadata Files:
- Readme: README.rst
Awesome Lists containing this project
README
.. image:: /ONT_logo.png
:width: 800
******************
Rerio
"""""
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.
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)
**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 Dorado executable.
See further details for running Dorado `here `_.
Dependencies
------------
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 `_.
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/dorado_models/res_dna_r10.4.1_e8.2_400bps_sup@v4.0.1_url
*******************
Dorado Models
-------------
==================================================================== ======= ============ ====== ============= ==================================================================================
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
res_dna_r10.4.1_e8.2_400bps_sup\@v4.0.1 DNA R10.4.1 E8.2 All v0.3.0 Kit 14 4kHz Model Compatible with All-context Modified Bases
res_dna_r10.4.1_e8.2_400bps_sup\@v4.0.1_5mC@v2 DNA R10.4.1 E8.2 All v0.3.0 Kit 14 4kHz 5mC All-context Modified Base Model
res_dna_r10.4.1_e8.2_400bps_sup\@v4.0.1_6mA@v2 DNA R10.4.1 E8.2 All v0.3.0 Kit 14 4kHz 6mA All-context Modified Base Model
res_dna_r10.4.1_e8.2_400bps_sup\@v4.3.0_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/res_dna_r10.4.1_e8.2_400bps_sup@v4.3.0_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
-------------
Clair3 models for the following configurations are available:
Latest:
========================== =================== =======================
Config Chemistry Dorado basecaller model
========================== =================== =======================
r1041_e82_400bps_sup_v520 R10.4.1 E8.2 (5kHz) v5.2.0 SUP
r1041_e82_400bps_hac_v520 R10.4.1 E8.2 (5kHz) v5.2.0 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}``.
*********************
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.
=============================================== ======= ======== ============== ============ ==========================
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.
*******************
Guppy models
----------------------------------------
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
=============================================== ======= ====== ============== ============ ==========================
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
Licence and Copyright
---------------------
|copy| 2020-2023 Oxford Nanopore Technologies Ltd.
.. |copy| unicode:: 0xA9 .. copyright sign
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.