Trans-Omics Acceleration Library

Introduction

The Trans-Omics Acceleration Library (TAL) contains key modules for Trans-Omics analysis that are optimized for Xeon.

The contributors to TAL are Sanchit Misra, Vasimuddin Md, Saurabh Kalikar, Narendra Chaudhary and Kanak Mahadik.

The following block diagram illustrates the building blocks and applications available in TAL.

Getting Started

git clone --recursive <REPO URL>
make

Publications

Narendra Chaudhary, Sanchit Misra, Dhiraj Kalamkar, Alexander Heinecke, Evangelos Georganas, Barukh Ziv, Menachem Adelman and Bharat Kaul. Accelerating Deep Learning based Identification of Chromatin Accessibility from noisy ATAC-seq Data. 21st IEEE International Workshop on High Performance Computational Biology (HiCOMB) May 30, 2022. https://ieeexplore.ieee.org/abstract/document/9835674

Saurabh Kalikar, Chirag Jain, Md Vasimuddin, Sanchit Misra. Accelerating minimap2 for long-read sequencing applications on modern CPUs. Nature Computational Science 2 (2), 78-83, Feb, 2022. https://rdcu.be/cHVAK.

Narendra Chaudhary, Sanchit Misra, Dhiraj Kalamkar, Alexander Heinecke, Evangelos Georganas, Barukh Ziv, Menachem Adelman, Bharat Kaul. Efficient and generic 1d dilated convolution layer for deep learning. arXiv preprint arXiv:2104.08002, 2021.

Darryl Ho, Saurabh Kalikar, Sanchit Misra, Jialin Ding, Vasimuddin Md, Nesime Tatbul, Heng Li, Tim Kraska. LISA: Learned indexes for sequence analysis. bioRxiv 2020.12.22.423964; doi: https://doi.org/10.1101/2020.12.22.423964.

Vasimuddin Md, Sanchit Misra, Heng Li, Srinivas Aluru. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE Parallel and Distributed Processing Symposium (IPDPS), 2019.

Sanchit Misra, Tony Pan, Kanak Mahadik, George Powley, Priya N Vaidya, Md Vasimuddin, Srinivas Aluru. Performance extraction and suitability analysis of multi- and many-core architectures for next generation sequencing secondary analysis. International Conference on Parallel Architectures and Compilation Techniques (PACT), 2018.

Md Vasimuddin, Sanchit Misra, Srinivas Aluru.
Identification of Significant Computational Building Blocks through Comprehensive Deep Dive of NGS Secondary Analysis Methods. BioRxiv 2018 301903. https://www.biorxiv.org/content/10.1101/301903v3.abstract.