{"id":19984536,"url":"https://github.com/intellabs/trans-omics-acceleration-library","last_synced_at":"2026-03-09T14:04:55.277Z","repository":{"id":43382728,"uuid":"277848874","full_name":"IntelLabs/Trans-Omics-Acceleration-Library","owner":"IntelLabs","description":null,"archived":false,"fork":false,"pushed_at":"2024-05-30T09:01:25.000Z","size":42067,"stargazers_count":15,"open_issues_count":2,"forks_count":5,"subscribers_count":17,"default_branch":"master","last_synced_at":"2025-01-12T11:20:21.002Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/IntelLabs.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-07-07T15:06:26.000Z","updated_at":"2024-05-30T09:01:30.000Z","dependencies_parsed_at":"2025-01-12T11:30:19.168Z","dependency_job_id":null,"html_url":"https://github.com/IntelLabs/Trans-Omics-Acceleration-Library","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IntelLabs%2FTrans-Omics-Acceleration-Library","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IntelLabs%2FTrans-Omics-Acceleration-Library/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IntelLabs%2FTrans-Omics-Acceleration-Library/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IntelLabs%2FTrans-Omics-Acceleration-Library/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/IntelLabs","download_url":"https://codeload.github.com/IntelLabs/Trans-Omics-Acceleration-Library/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241419111,"owners_count":19959856,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-13T04:19:25.809Z","updated_at":"2026-03-09T14:04:50.225Z","avatar_url":"https://github.com/IntelLabs.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Trans-Omics Acceleration Library\n\n## Introduction\nThe Trans-Omics Acceleration Library (TAL) contains key modules for Trans-Omics analysis that are optimized for Xeon.\n\nThe contributors to TAL are Sanchit Misra, Vasimuddin Md, Saurabh Kalikar, Narendra Chaudhary and Kanak Mahadik.\n\nThe following block diagram illustrates the building blocks and applications available in TAL.\n\u003cp align=\"center\"\u003e\n\u003cimg src=\"https://github.com/IntelLabs/Trans-Omics-Acceleration-Library/blob/master/images/trans-omics-acceleration-lib.jpg\" height=\"300\"/a\u003e\u003c/br\u003e\n\u003c/p\u003e \n\n\n## Getting Started\n```sh\ngit clone --recursive \u003cREPO URL\u003e\nmake\n```\n\n## Publications\n\nNarendra Chaudhary, Sanchit Misra, Dhiraj Kalamkar, Alexander Heinecke, Evangelos Georganas, Barukh Ziv, Menachem Adelman and Bharat Kaul.\n\u003cb\u003e Accelerating Deep Learning based Identification of Chromatin Accessibility from noisy ATAC-seq Data. \u003c/b\u003e\n\u003ci\u003e 21st IEEE International Workshop on High Performance Computational Biology (HiCOMB) May 30, 2022. https://ieeexplore.ieee.org/abstract/document/9835674 \u003c/i\u003e\n\nSaurabh Kalikar, Chirag Jain, Md Vasimuddin, Sanchit Misra.\n\u003cb\u003e Accelerating minimap2 for long-read sequencing applications on modern CPUs. \u003c/b\u003e\n\u003ci\u003e Nature Computational Science 2 (2), 78-83, Feb, 2022. https://rdcu.be/cHVAK. \u003c/i\u003e\n\nNarendra Chaudhary, Sanchit Misra, Dhiraj Kalamkar, Alexander Heinecke, Evangelos Georganas, Barukh Ziv, Menachem Adelman, Bharat Kaul.\n\u003cb\u003e Efficient and generic 1d dilated convolution layer for deep learning. \u003c/b\u003e\n\u003ci\u003e arXiv preprint arXiv:2104.08002, 2021. \u003c/i\u003e\n\nDarryl Ho, Saurabh Kalikar, Sanchit Misra, Jialin Ding, Vasimuddin Md, Nesime Tatbul, Heng Li, Tim Kraska. \n\u003cb\u003e LISA: Learned indexes for sequence analysis. \u003c/b\u003e\n\u003ci\u003e bioRxiv 2020.12.22.423964; doi: https://doi.org/10.1101/2020.12.22.423964. \u003c/i\u003e\n\nVasimuddin Md, Sanchit Misra, Heng Li, Srinivas Aluru.\n\u003cb\u003e Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. \u003c/b\u003e\n\u003ci\u003e IEEE Parallel and Distributed Processing Symposium (IPDPS), 2019. \u003c/i\u003e\n\nSanchit Misra, Tony  Pan, Kanak  Mahadik, George  Powley, Priya N Vaidya, Md  Vasimuddin, Srinivas  Aluru.\n\u003cb\u003e Performance extraction and suitability analysis of multi- and many-core architectures for next generation sequencing secondary analysis. \u003c/b\u003e\n\u003ci\u003e International Conference on Parallel Architectures and Compilation Techniques (PACT), 2018. \u003c/i\u003e\n\n\nMd Vasimuddin, Sanchit Misra, Srinivas Aluru.  \n\u003cb\u003e Identification of Significant Computational Building Blocks through Comprehensive Deep Dive of NGS Secondary Analysis Methods. \u003c/b\u003e\n\u003ci\u003e BioRxiv 2018 301903. https://www.biorxiv.org/content/10.1101/301903v3.abstract. \u003c/i\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fintellabs%2Ftrans-omics-acceleration-library","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fintellabs%2Ftrans-omics-acceleration-library","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fintellabs%2Ftrans-omics-acceleration-library/lists"}