.. image:: /ONT_logo.png :width: 800 ****************** Rerio """"" Rerio is comprised of "research release" basecalling models and configuration files. All 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_r941_min_modbases-all-context_v001 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_r941_min_modbases-all-context_v001.cfg ************** Use and description of basecaller models ---------------------------------------- =============================================== ======= ====== ============== ============ ========================== 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_modbases_5mC_v001.cfg DNA R9.4.1 MinION/GridION v4.2.2 5mC in all context res_dna_r941_prom_modbases_5mC_v001.cfg DNA R9.4.1 PromethION v4.2.2 5mC in all context res_dna_r103_prom_modbases_5mC_v001.cfg DNA R10.3 PromethION v4.2.2 5mC in all context res_dna_r941_min_modbases_5mC_5hmC_v001.cfg DNA R9.4.1 MinION/GridION v4.2.2 5hmC & 5mC in all context 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 res_dna_r941_min_modbases-all-context_v001.cfg DNA R9.4.1 MinION/GridION v3.5.1 5mC & 6mA in all contexts =============================================== ======= ====== ============== ============ ========================== 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_r941_min_modbases_5mC_5hmC_CpG_v001.cfg \ --mod-motif mh CG 0 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 taiyaki_checkpoint/model ********************* Clair3 Models ------------- Clair3 models for the following configurations are available: ================== ========== ================ Config Chemistry Guppy basecaller ================== ========== ================ 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_models.py --clair3 # Download particular model python3 download_models.py clair3_models/model Each model will be downloaded to the folder ``clair3_models/ont_{config}``. ******* Help """" Licence and Copyright --------------------- |copy| 2020, 2021 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.