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GPU beamsearch decoding for nanopore basecalling

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openfish

Openfish is a submodule used in slorado for performing beamsearch decoding. The CPU implementation written in C was adopted from the C++ beamsearch implementation in ONT Dorado which is licensed under the Oxford Nanopore Technologies PLC. Public License Version 1.0. Then based on that C implementation, we implemented the GPU version for NVIDIA GPUs using CUDA C and for AMD GPUs using HIP C.

This is in early stages of development and thus the API not at all stable (and thus not documented).

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GPU beamsearch decoding for nanopore basecalling

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