Samtool Supported Models May 2026

SAMtools has evolved significantly to support Pacific Biosciences data, particularly the HiFi (Circular Consensus Sequencing) model.

The original models released by Meta AI Research (FAIR). samtool supported models

| Model ID | Architecture | Backbone | Output Mask Quality | Speed | Use Case | | :--- | :--- | :--- | :--- | :--- | :--- | | sam_vit_b | ViT-Base | 80M params | High | Fast | Edge devices, real-time apps | | sam_vit_l | ViT-Large | 300M params | Higher | Medium | General purpose | | sam_vit_h | ViT-Huge | 636M params | Highest | Slow | High-precision annotation | The original models released by Meta AI Research (FAIR)

Load syntax:

samtool.load_model("sam_vit_h", checkpoint="sam_vit_h_4b8939.pth")

The list above only represents model architectures. Samtool’s true power lies in mapping these models to specific hardware. The supported models run on the following backends: The list above only represents model architectures

For each target, Samtool validates operator support at compile time. If an operator is missing, it can often be decomposed into simpler ops or run as a microkernel.

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