From 0eaf4282a4fc4f0e864a186a0d967341cee2e0be Mon Sep 17 00:00:00 2001 From: sanchit-misra Date: Wed, 22 Nov 2023 15:54:04 +0530 Subject: [PATCH] Update README.md --- README.md | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 47c8c93..50cec4b 100644 --- a/README.md +++ b/README.md @@ -18,6 +18,22 @@ With a goal to build a performant, cost effective and productive platform, we ar

+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 @@ -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 ```