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Revio clarifications
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armintoepfer committed Mar 18, 2024
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Expand Up @@ -11,15 +11,15 @@ longer stored, nor can be transferred, as file sizes exceed one TBytes per
SMRT Cell 25M. Aside constant algorithmic improvements, there are few changes
since the 6.4.0 SQIIe release.

1. Arrow polishing is performed on the instrument.
2. DeepConsensus further increases quality of lower quality windows.
1. Arrow polishing is performed on GPU.
2. DeepConsensus further increases accuracy of lower quality windows.
3. Performance improvements.
4. The customer-facing files layout changed.
5. A new `fail_reads.bam` has been introduced.

### GPU polishing
<p align="left"><img width="350px" src="../img/arrow-gpu.png" style="float: left; margin:0 30px 10px 0px "/>
The polish algo in _ccs_ is an HMM, filling out matrices at its core. The nature
The polish algo in <i>ccs</i> is an HMM, filling out matrices at its core. The nature
of its operations makes an efficient GPU implementation challenging. We’ve
ported it completely onto Nvidia GPUs and achieved a 10x speedup over a dual
64c AMD EPYC, easily the fastest HMM on GPU.</p>
Expand All @@ -28,7 +28,7 @@ ported it completely onto Nvidia GPUs and achieved a 10x speedup over a dual
### DeepConsensus
We have tightly integrate Google's [DeepConsensus](https://github.com/google/deepconsensus)
into _ccs_. For this, we have implemented a C++ front-end using ONNXruntime
and accelerate it on TensorRT cores of modern data center Nvidia GPU cards.
and accelerated it on TensorRT cores of modern data center Nvidia GPU cards.
HiFi read generation on the Revio system uses a multi-step process, which
also has an impact how the predicted read quality is computed:

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