Clair3 and Clair3-RNA
Clair3-RNA is a specialized adaptation of the base Clair3 variant caller specifically optimized for RNA sequencing data, making them complementary tools for different input types rather than competitors.
About Clair3
HKU-BAL/Clair3
Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling
Employs a dual-model architecture combining fast pileup-based calling with computationally intensive full-alignment models for complex variants, optimizing both speed and accuracy across coverage depths. Recently migrated to PyTorch with GPU acceleration (~5x speedup on Linux/Apple Silicon) and added signal-aware variant calling via Dorado move tables. Provides pre-trained models for multiple sequencing chemistries (Guppy 2-6, R10.4 Q20) and supports both standard germline VCF/GVCF output with modular training pipelines for custom datasets.
About Clair3-RNA
HKU-BAL/Clair3-RNA
Clair3-RNA - a long-read small variant caller for RNA sequencing data
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