Clair3 Models
Overview
The pipeline uses Clair3 for variant calling. Clair3 requires a model that matches the pore chemistry and basecalling preset used to produce the input reads. Models are downloaded from the HKU Clair3 model repository and stored as PyTorch checkpoints (pileup.pt and full_alignment.pt).
Downloading models
artic_get_models --models r1041_e82_400bps_sup_v400 r1041_e82_400bps_sup_v420 ...
Will fetch the models provided as a space-delimited list to the --models parameter, if no --models parameter is provided all models will be fetched.
Models are stored in $CONDA_PREFIX/bin/models/ by default. For a custom location:
artic_get_models --model-dir /path/to/models
The *-models-included Docker image variant bundles all models. The default Docker image does not include models — use --model-dir to mount a pre-downloaded model directory. artic_get_models is needed for conda/source installs and to prepare models for use with the default Docker image.
Automatic model selection
When --model is not provided, the pipeline extracts the basecalling model from the first read in the input FASTQ and selects a Clair3 model automatically. Two header formats are supported.
Old format (Dorado < 2.0.0, space-separated key=value pairs):
@read1 basecall_model_version_id=dna_r10.4.1_e8.2_400bps_hac@v5.2.0 ...
New format (Dorado ≥ 2.0.0, SAM-style tab-separated tags):
@read1 qs:f:17.57 RG:Z:87a1966c-..._dna_r10.4.1_e8.2_400bps_hac@v5.2.0_barcode01 ...
In the new format the basecalling model is embedded in the RG:Z tag value as <run-id>_<model>_<barcode>. Both formats are detected automatically — no configuration is required.
The selection algorithm:
- Extracts the model string (e.g.
dna_r10.4.1_e8.2_400bps_hac@v5.2.0) from whichever header format is present. - Splits the model string on
_to extract pore type, kit ID, speed tier, and basecaller version. - Filters available models by pore type and speed tier.
- Matches the basecaller version string (e.g.
v520for Dorado 5.2.0). - If exactly one model matches at each step it is selected and a warning is printed. If no match is found at any step the pipeline exits with code 6.
Use --model to override auto-selection at any time.
Guppy vs Dorado compatibility
Clair3 models whose names contain a g-prefixed version suffix (e.g. _g632, _g5014) were trained on data basecalled with Guppy. These models are not compatible with Dorado-basecalled data and will produce incorrect variant calls if used with it.
If you see exit code 6 for a fast-mode Dorado model: no versioned Clair3 fast model exists for R10.4.1 data. Re-basecall with hac or sup.
Available models
Dorado models
These models correspond to data basecalled with Dorado. The Dorado basecall model column shows the dorado basecalling model tag value that will auto-select each model.
R10.4.1 — 400 bps
| Clair3 model | Dorado basecalling model |
|---|---|
r1041_e82_400bps_hac_v600 |
dna_r10.4.1_e8.2_400bps_hac@v6.0.0 |
r1041_e82_400bps_hac_v520 |
dna_r10.4.1_e8.2_400bps_hac@v5.2.0 |
r1041_e82_400bps_sup_v520 |
dna_r10.4.1_e8.2_400bps_sup@v5.2.0 |
r1041_e82_400bps_hac_v500 |
dna_r10.4.1_e8.2_400bps_hac@v5.0.0 |
r1041_e82_400bps_sup_v500 |
dna_r10.4.1_e8.2_400bps_sup@v5.0.0 |
r1041_e82_400bps_hac_v430 |
dna_r10.4.1_e8.2_400bps_hac@v4.3.0 |
r1041_e82_400bps_sup_v430 |
dna_r10.4.1_e8.2_400bps_sup@v4.3.0 |
r1041_e82_400bps_hac_v420 |
dna_r10.4.1_e8.2_400bps_hac@v4.2.0 |
r1041_e82_400bps_sup_v420 |
dna_r10.4.1_e8.2_400bps_sup@v4.2.0 |
r1041_e82_400bps_hac_v410 |
dna_r10.4.1_e8.2_400bps_hac@v4.1.0 |
r1041_e82_400bps_sup_v410 |
dna_r10.4.1_e8.2_400bps_sup@v4.1.0 |
r1041_e82_400bps_hac_v400 |
dna_r10.4.1_e8.2_400bps_hac@v4.0.0 |
r1041_e82_400bps_sup_v400 |
dna_r10.4.1_e8.2_400bps_sup@v4.0.0 |
Warning
No versioned Clair3 fast models exist for R10.4.1 data. Reads basecalled with dna_r10.4.1_e8.2_400bps_fast@vX.Y.Z cannot be automatically matched to a model. Re-basecall with hac or sup.
R10.4.1 — 260 bps
| Clair3 model | Dorado basecalling model |
|---|---|
r1041_e82_260bps_hac_v410 |
dna_r10.4.1_e8.2_260bps_hac@v4.1.0 |
r1041_e82_260bps_sup_v410 |
dna_r10.4.1_e8.2_260bps_sup@v4.1.0 |
r1041_e82_260bps_hac_v400 |
dna_r10.4.1_e8.2_260bps_hac@v4.0.0 |
r1041_e82_260bps_sup_v400 |
dna_r10.4.1_e8.2_260bps_sup@v4.0.0 |
R9.4.1
| Clair3 model | Dorado basecalling model |
|---|---|
r941_prom_hac_g360+g422 |
dna_r9.4.1_e8_hac@vX.X |
r941_prom_sup_g5014 |
dna_r9.4.1_e8_sup@vX.X |
R9.4.1 has only two models (one per preset). Auto-selection returns the correct model for any R9.4.1 hac or sup tag regardless of basecaller version.
Guppy models (legacy)
These models were trained on data basecalled with Guppy. They are not compatible with Dorado-basecalled data. Use them only if your reads were produced by Guppy.
R10.4.1 — 400 bps
| Clair3 model | Guppy version | Preset |
|---|---|---|
r1041_e82_400bps_hac_g632 |
g632 | hac |
r1041_e82_400bps_hac_g615 |
g615 | hac |
r1041_e82_400bps_sup_g615 |
g615 | sup |
r1041_e82_400bps_fast_g632 |
g632 | fast |
r1041_e82_400bps_fast_g615 |
g615 | fast |
R10.4.1 — 260 bps
| Clair3 model | Guppy version | Preset |
|---|---|---|
r1041_e82_260bps_hac_g632 |
g632 | hac |
r1041_e82_260bps_sup_g632 |
g632 | sup |
r1041_e82_260bps_fast_g632 |
g632 | fast |
R10.4 (E8.1)
| Clair3 model | Guppy version | Preset |
|---|---|---|
r104_e81_hac_g5015 |
g5015 | hac |
r104_e81_sup_g5015 |
g5015 | sup |