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sanchit-misra authored Nov 22, 2023
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Expand Up @@ -18,6 +18,22 @@ With a goal to build a performant, cost effective and productive platform, we ar
<img src="https://github.com/IntelLabs/Open-Omics-Acceleration-Framework/blob/main/images/Open-Omics-Acceleration-Framework-v2.0.JPG" height="300"/a></br>
</p>

With a goal of providing a one-stop platform, this framework brings our following repositories for digital biology under one umbrella:
* Architecture efficient versions of several popular applications as part of our toolkit layer

| Original Application | Our architecure-efficient version |
| --- | --- |
| Short read sequence mapping tool, [BWA-MEM](https://github.com/lh3/bwa) | [BWA-MEM2](https://github.com/bwa-mem2/bwa-mem2) |
| long read sequence mapping tool, [minimap2](https://github.com/lh3/minimap2) | [mm2-fast](https://github.com/bwa-mem2/mm2-fast) |
| Deep learning based variant calling tool, [DeepVariant](https://github.com/google/deepvariant) | [Open-Omics-DeepVariant](https://github.com/IntelLabs/open-omics-deepvariant) |
| Deep learning based tool for protein structure prediction, [AlphaFold2](https://github.com/google-deepmind/alphafold) | [Open-Omics-AlphaFold](https://github.com/IntelLabs/open-omics-alphafold) |
| Tool for biological sequence analysis using profile HMMs, [HMMER](https://github.com/EddyRivasLab/hmmer) | [IntelLabs HMMER](https://github.com/IntelLabs/hmmer) |
| Tool for HMM based sensitive protein sequence searching, [HH-suite](https://github.com/soedinglab/hh-suite) | [IntelLabs HH-suite](https://github.com/IntelLabs/hh-suite) |

* [Trans-Omics Acceleration Library](https://github.com/IntelLabs/Trans-Omics-Acceleration-Library): As part of our building blocks layer, this is a library containing architecture-efficient versions of key algorithms and data structures used for Omics analysis.

In addition, we also use several existing AI libraries: oneDNN, oneDAL, oneCCL, Katana Graph, LIBXSMM.

# Getting Started
```sh
# Download release
Expand All @@ -34,7 +50,7 @@ cd pipelines
# Go to the directory with toolkit
cd applications

# Go to the directory with biology building blocks
# Go to the directory with biology building blocks to access Trans-Omics Acceleration Library
cd lib/tal

```
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