{"id":25596849,"url":"https://github.com/nanoporetech/rerio","last_synced_at":"2025-09-05T16:06:26.397Z","repository":{"id":41174905,"uuid":"248183660","full_name":"nanoporetech/rerio","owner":"nanoporetech","description":"Research release basecalling models and configurations","archived":false,"fork":false,"pushed_at":"2024-06-18T20:48:01.000Z","size":122,"stargazers_count":108,"open_issues_count":4,"forks_count":10,"subscribers_count":33,"default_branch":"master","last_synced_at":"2025-04-06T08:02:15.697Z","etag":null,"topics":["basecalling","nanopore"],"latest_commit_sha":null,"homepage":"https://nanoporetech.com/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/nanoporetech.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-03-18T09:05:35.000Z","updated_at":"2025-04-03T07:50:45.000Z","dependencies_parsed_at":"2024-05-21T19:34:17.184Z","dependency_job_id":"a0da0113-4510-4f41-aa8c-57496165d310","html_url":"https://github.com/nanoporetech/rerio","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanoporetech%2Frerio","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanoporetech%2Frerio/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanoporetech%2Frerio/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanoporetech%2Frerio/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nanoporetech","download_url":"https://codeload.github.com/nanoporetech/rerio/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248657795,"owners_count":21140841,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["basecalling","nanopore"],"created_at":"2025-02-21T12:34:48.794Z","updated_at":"2025-09-05T16:06:26.377Z","avatar_url":"https://github.com/nanoporetech.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":".. image:: /ONT_logo.png\n  :width: 800\n\n******************\n\nRerio\n\"\"\"\"\"\n\nRerio is comprised of \"research release\" basecalling models and configuration files.\n\nThe research models provide cutting-edge functions, speeds and accuracies that have not been productionised or validated by Oxford Nanopore Technologies.\nNevertheless, models and config files can be run by using the instructions available in this repository.\n\nModels are provided for DNA and RNA, various pore types and to basecall different modified bases in a variety of contexts.\n\nFeatures\n--------\n\n- 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)\n\n**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)\n\n*********************\n\nGetting started\n\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\n\nFollow the instructions below to use research models with Dorado executable.\nSee further details for running Dorado `here \u003chttps://github.com/nanoporetech/dorado\u003e`_.\n\nDependencies\n------------\n\nYou will require:\n\n- Python-compatible environment (e.g. Terminal)\n- The most recent Dorado version, available on the Nanopore Community `Software downloads page \u003chttps://community.nanoporetech.com/downloads\u003e`_ or the `Dorado GitHub page \u003chttps://github.com/nanoporetech/dorado\u003e`_.\n\n\nInstallation\n------------\n\nRerio can be downloaded by cloning from GitHub ``git clone https://github.com/nanoporetech/rerio``.\nOnce Rerio has been downloaded, models can be downloaded via the ``download_model.py`` script.\n\n::\n\n   # Download all models\n   rerio/download_model.py\n   # Download specific model(s)\n   rerio/download_model.py rerio/dorado_models/res_dna_r10.4.1_e8.2_400bps_sup@v4.0.1_url\n\n*******************\n\nDorado Models\n-------------\n\n==================================================================== ======= ============ ====== ============= ==================================================================================\nConfig                                                               DNA/RNA Chemistry    Device Tested Dorado Notes\n==================================================================== ======= ============ ====== ============= ==================================================================================\nres_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\nres_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\nres_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\nres_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\nres_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\n==================================================================== ======= ============ ====== ============= ==================================================================================\n\n::\n\n    #  Download all models\n    python3 download_model.py --dorado\n    #  Download particular model\n    python3 download_model.py --dorado dorado_models/res_dna_r10.4.1_e8.2_400bps_sup@v4.3.0_4mC_5mC@v1_url\n\nEach model will be downloaded to ``dorado_models/{config}``.\n\nBasecalling models can be supplied directly to `Dorado \u003chttps://github.com/nanoporetech/dorado\u003e`_. Please refer to the Dorado README for more information on how to run basecalling and use modified base models. \n\n\n*********************\n\nClair3 Models\n-------------\n\nClair3 models for the following configurations are available:\n\nLatest:\n\n========================== =================== =======================\nConfig                     Chemistry           Dorado basecaller model\n========================== =================== =======================\nr1041_e82_400bps_sup_v520  R10.4.1 E8.2 (5kHz) v5.2.0 SUP\nr1041_e82_400bps_hac_v520  R10.4.1 E8.2 (5kHz) v5.2.0 HAC\nr1041_e82_400bps_sup_v410  R10.4.1 E8.2 (4kHz) v4.1.0 SUP\nr1041_e82_400bps_hac_v410  R10.4.1 E8.2 (4kHz) v4.1.0 HAC\n========================== =================== =======================\n\nDeprecated:\n\n========================== =================== ======================= ================\nConfig                     Chemistry           Dorado basecaller model Guppy basecaller\n========================== =================== ======================= ================\nr1041_e82_400bps_sup_v430  R10.4.1 E8.2 (5kHz) v4.3.0 SUP                              \nr1041_e82_400bps_hac_v430  R10.4.1 E8.2 (5kHz) v4.3.0 HAC                              \nr1041_e82_400bps_sup_v420  R10.4.1 E8.2 (5kHz) v4.2.0 SUP                              \nr1041_e82_400bps_hac_v420  R10.4.1 E8.2 (5kHz) v4.2.0 HAC                              \nr1041_e82_260bps_sup_v400  R10.4.1 E8.2        v4.0.0 SUP              -               \nr1041_e82_260bps_hac_v400  R10.4.1 E8.2        v4.0.0 HAC              -               \nr1041_e82_260bps_fast_g632 R10.4.1 E8.2        v3.5.2 FAST             v6.3.2 FAST     \nr1041_e82_400bps_sup_g615  R10.4.1 E8.2        v3.5.2 SUP              v6.1.5 SUP      \nr1041_e82_400bps_hac_g632  R10.4.1 E8.2        v3.5.2 HAC              v6.3.2 HAC      \nr1041_e82_400bps_hac_g615  R10.4.1 E8.2        -                       v6.1.5 HAC      \nr1041_e82_400bps_fast_g615 R10.4.1 E8.2        -                       v6.1.5 FAST     \nr1041_e82_260bps_sup_g632  R10.4.1 E8.2        v3.5.2 SUP              v6.3.2 SUP      \nr1041_e82_260bps_hac_g632  R10.4.1 E8.2        v3.5.2 HAC              v6.3.2 HAC      \nr1041_e82_400bps_fast_g632 R10.4.1 E8.2        v3.5.2 FAST             -               \nr104_e81_sup_g5015         R10.4 E8.1          -                       v5.0.15 SUP     \nr104_e81_hac_g5015         R10.4 E8.1          -                       v5.0.15 HAC     \n========================== =================== ======================= ================\n\n::\n\n    #  Download all models\n    python3 download_model.py --clair3\n    #  Download particular model\n    python3 download_model.py --clair3 clair3_models/{config}_model\n\nEach model will be downloaded to the folder ``clair3_models/{config}``.\n\n*********************\n\nRemora Models\n-------------\n\nMost Remora models are supplied along with the `Remora repository \u003chttps://github.com/nanoporetech/remora\u003e`_, but models with less validation intended for research purposes will be released in Rerio.\n\n=============================================== ======= ======== ============== ============ ==========================\nConfig                                          DNA/RNA Pore     Device         Tested Guppy Notes\n=============================================== ======= ======== ============== ============ ==========================\n5mC_all_context_sup_r1041_e82                   DNA     R10.4.1  Any            v6.1.2       5mC in all context (with SUP basecaller)\n=============================================== ======= ======== ============== ============ ==========================\n\n::\n\n    #  Download all models\n    python3 download_model.py --remora\n    #  Download particular model\n    python3 download_model.py --remora remora_models/5mC_all_context_sup_r1041_e82\n\nEach model will be downloaded to ``remora_models/{config}.pt`` (or ``remora_models/{config}.onnx`` for Remora version \u003c2.0).\n\nThese models can be supplied directly to `Bonito \u003chttps://github.com/nanoporetech/bonito\u003e`_ via the ``--modified-base-model`` argument.\n\n*******************\n\nGuppy models\n----------------------------------------\n\nThis section contains research release Guppy compatible models.\nSee `Nanopore Community page \u003chttps://community.nanoporetech.com/downloads\u003e`_ for download/install instructions.\nSince research models often utilise new features, the latest version of Guppy may be required.\n\n=============================================== ======= ====== ============== ============ ==========================\nConfig                                          DNA/RNA Pore   Device         Tested Guppy Notes\n=============================================== ======= ====== ============== ============ ==========================\nres_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\nres_dna_r941_min_crf_v032.cfg                   DNA     R9.4.1 MinION/GridION v4.4.0       Bonito CRF\nres_dna_r103_min_crf_v032.cfg                   DNA     R10.3  MinION/GridION v4.4.0       Bonito CRF\nres_dna_r103_q20ea_crf_v033.cfg                 DNA     R10.3  PromethION     v5.0.11      Q20 early access CRF\nres_dna_r103_q20ea_crf_v034.cfg                 DNA     R10.3  PromethION     v5.0.11      Q20 early access CRF\nres_dna_r941_min_flipflop_v001.cfg              DNA     R9.4.1 MinION/GridION v3.5.1\nres_dna_r941_min_dUfast_v001.cfg                DNA     R9.4.1 MinION/GridION v3.5.1       Calls dU as dT (fast)\nres_dna_r941_min_dUhac_v001.cfg                 DNA     R9.4.1 MinION/GridION v3.5.1       Calls dU as dT (high acc.)\nres_dna_r941_min_rle_v001.cfg                   DNA     R9.4.1 MinION/GridION v3.5.1\nres_dna_r103_min_flipflop_v001.cfg              DNA     R10.3  MinION/GridION v3.5.1\nres_dna_r103_prom_rle_v001.cfg                  DNA     R10.3  PromethION     v3.5.1\nres_rna2_r941_min_flipflop_v001.cfg             RNA2    R9.4.1 MinION/GridION v3.5.1\n=============================================== ======= ====== ============== ============ ==========================\n\nBarcoding Support\n-----------------\n\nThe Rerio GitHub code repository includes a minimal barcoding stub to allow Guppy to run successfully.\nIn order to enable full Guppy barcoding capabilities, all barcoding files must be transferred from the guppy data directory to the rerio data directory.\n\n::\n\n   cp ont-guppy/data/barcoding/* rerio/basecall_models/barcoding/\n\nTaiyaki Models\n--------------\n\nTaiyaki checkpoint files corresponding to Rerio research models are provided.\nNot all of these are compatible with the public release of Taiyaki.\n\n::\n\n    #  Download all models\n    python3 download_models.py --checkpoints\n    #  Download particular model\n    python3 download_models.py --checkpoints taiyaki_checkpoint/model\n\nLicence and Copyright\n---------------------\n\n|copy| 2020-2023 Oxford Nanopore Technologies Ltd.\n\n.. |copy| unicode:: 0xA9 .. copyright sign\n\nRerio is distributed under the terms of the Oxford Nanopore\nTechnologies, Ltd.  Public License, v. 1.0.  If a copy of the License\nwas not distributed with this file, You can obtain one at\nhttp://nanoporetech.com\n\n\nResearch Release\n^^^^^^^^^^^^^^^^\n\nResearch 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.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnanoporetech%2Frerio","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnanoporetech%2Frerio","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnanoporetech%2Frerio/lists"}