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Dorado container

Main tool: dorado

Code repository: https://github.com/nanoporetech/dorado

Basic information on how to use this tool:

executable: dorado
help: -h, --help
version: -v, --version
description: Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.

Additional information:

Cuda drivers >= 12.2.0 are required for gpu support.
Use "--gpus all" flag to activate gpu support in docker. E.g. docker run -it --gpus all staphb/dorado:1.1.0-cuda12.2.0-no_model bash
support for Fast5 files and basecalling models for DNA R10.4.1 4kHz data, DNA R9.4.1, and RNA002 were removed after v0.9.6
Below is the list of basecalling models included in the Docker image:

Click to see all models

variant models:
  - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_variant_mv@v1.0"
correction models:
  - "herro-v1"
simplex models:
  - "dna_r10.4.1_e8.2_400bps_fast@v4.2.0"
  - "dna_r10.4.1_e8.2_400bps_hac@v4.2.0"
  - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0"
  - "dna_r10.4.1_e8.2_400bps_fast@v4.3.0"
  - "dna_r10.4.1_e8.2_400bps_hac@v4.3.0"
  - "dna_r10.4.1_e8.2_400bps_sup@v4.3.0"
  - "dna_r10.4.1_e8.2_400bps_fast@v5.0.0"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0"
  - "dna_r10.4.1_e8.2_apk_sup@v5.0.0"
  - "dna_r10.4.1_e8.2_400bps_fast@v5.2.0"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.2.0"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.2.0"
  - "rna004_130bps_fast@v3.0.1"
  - "rna004_130bps_hac@v3.0.1"
  - "rna004_130bps_sup@v3.0.1"
  - "rna004_130bps_fast@v5.0.0"
  - "rna004_130bps_hac@v5.0.0"
  - "rna004_130bps_sup@v5.0.0"
  - "rna004_130bps_fast@v5.1.0"
  - "rna004_130bps_hac@v5.1.0"
  - "rna004_130bps_sup@v5.1.0"
  - "rna004_130bps_fast@v5.2.0"
  - "rna004_130bps_hac@v5.2.0"
  - "rna004_130bps_sup@v5.2.0"
polish models:
  - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_polish_rl"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_polish_rl_mv"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_polish_rl"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_polish_rl_mv"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.2.0_polish_rl"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.2.0_polish_rl_mv"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.2.0_polish_rl"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.2.0_polish_rl_mv"
  - "dna_r10.4.1_e8.2_400bps_polish_bacterial_methylation_v5.0.0"
  - "dna_r10.4.1_e8.2_400bps_hac@v4.2.0_polish"
  - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_polish"
  - "dna_r10.4.1_e8.2_400bps_hac@v4.3.0_polish"
  - "dna_r10.4.1_e8.2_400bps_sup@v4.3.0_polish"
modification models:
  - "dna_r10.4.1_e8.2_400bps_fast@v4.2.0_5mCG_5hmCG@v2"
  - "dna_r10.4.1_e8.2_400bps_hac@v4.2.0_5mCG_5hmCG@v2"
  - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mCG_5hmCG@v2"
  - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mCG_5hmCG@v3.1"
  - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mC@v2"
  - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_6mA@v2"
  - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_6mA@v3"
  - "dna_r10.4.1_e8.2_400bps_sup@v4.2.0_5mC_5hmC@v1"
  - "dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mC_5hmC@v1"
  - "dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mC_5hmC@v1"
  - "dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v1"
  - "dna_r10.4.1_e8.2_400bps_sup@v4.3.0_6mA@v1"
  - "dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v2"
  - "dna_r10.4.1_e8.2_400bps_sup@v4.3.0_6mA@v2"
  - "dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mCG_5hmCG@v1"
  - "dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mCG_5hmCG@v1"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_4mC_5mC@v1"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v1"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_4mC_5mC@v2"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_4mC_5mC@v3"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v2"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v3"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mC_5hmC@v1"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v1"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mC_5hmC@v2"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mC_5hmC@v3"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v2.0.1"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v3"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mCG_5hmCG@v1"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mCG_5hmCG@v1"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mCG_5hmCG@v2"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mCG_5hmCG@v3"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mCG_5hmCG@v2.0.1"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mCG_5hmCG@v3"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_6mA@v1"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_6mA@v1"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_6mA@v2"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.0.0_6mA@v3"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_6mA@v2"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.0.0_6mA@v3"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.2.0_4mC_5mC@v1"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.2.0_4mC_5mC@v1"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.2.0_5mC_5hmC@v1"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.2.0_5mC_5hmC@v1"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.2.0_5mCG_5hmCG@v1"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.2.0_5mCG_5hmCG@v1"
  - "dna_r10.4.1_e8.2_400bps_hac@v5.2.0_6mA@v1"
  - "dna_r10.4.1_e8.2_400bps_sup@v5.2.0_6mA@v1"
  - "rna004_130bps_sup@v3.0.1_m6A_DRACH@v1"
  - "rna004_130bps_hac@v5.0.0_m6A@v1"
  - "rna004_130bps_sup@v5.0.0_m6A@v1"
  - "rna004_130bps_hac@v5.0.0_m6A_DRACH@v1"
  - "rna004_130bps_sup@v5.0.0_m6A_DRACH@v1"
  - "rna004_130bps_hac@v5.0.0_pseU@v1"
  - "rna004_130bps_sup@v5.0.0_pseU@v1"
  - "rna004_130bps_hac@v5.1.0_m5C@v1"
  - "rna004_130bps_sup@v5.1.0_m5C@v1"
  - "rna004_130bps_hac@v5.1.0_inosine_m6A@v1"
  - "rna004_130bps_sup@v5.1.0_inosine_m6A@v1"
  - "rna004_130bps_hac@v5.1.0_m6A_DRACH@v1"
  - "rna004_130bps_sup@v5.1.0_m6A_DRACH@v1"
  - "rna004_130bps_hac@v5.1.0_pseU@v1"
  - "rna004_130bps_sup@v5.1.0_pseU@v1"
  - "rna004_130bps_sup@v5.2.0_2OmeG@v1"
  - "rna004_130bps_hac@v5.2.0_m5C@v1"
  - "rna004_130bps_sup@v5.2.0_m5C_2OmeC@v1"
  - "rna004_130bps_hac@v5.2.0_inosine_m6A@v1"
  - "rna004_130bps_sup@v5.2.0_inosine_m6A_2OmeA@v1"
  - "rna004_130bps_hac@v5.2.0_m6A_DRACH@v1"
  - "rna004_130bps_sup@v5.2.0_m6A_DRACH@v1"
  - "rna004_130bps_hac@v5.2.0_pseU@v1"
  - "rna004_130bps_sup@v5.2.0_pseU_2OmeU@v1"
stereo models:
  - "dna_r10.4.1_e8.2_5khz_stereo@v1.1"
  - "dna_r10.4.1_e8.2_5khz_stereo@v1.2"
  - "dna_r10.4.1_e8.2_5khz_stereo@v1.3"
  - "dna_r10.4.1_e8.2_5khz_stereo@v1.4"

Full documentation: https://dorado-docs.readthedocs.io/en/latest/

Example Usage

# list models
dorado download --list
# download a single model
dorado download --model {model_name}
# download all models
dorado download
# basecaller
dorado basecaller {model} {data} > calls.bam

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