{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/algorithmic-improvement-and-gpu-acceleration","title":"Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm","arxiv_id":"2203.15561","date":"2022-03-28","proceeding":null,"authors":["Joël Lindegger","Damla Senol Cali","Mohammed Alser","Juan Gómez-Luna","Onur Mutlu"],"abstract":"We improve on GenASM, a recent algorithm for genomic sequence alignment, by significantly reducing its memory footprint and bandwidth requirement. Our algorithmic improvements reduce the memory footprint by 24$\\times$ and the number of memory accesses by 12$\\times$. We efficiently parallelize the algorithm for GPUs, achieving a 4.1$\\times$ speedup over a CPU implementation of the same algorithm, a 62$\\times$ speedup over minimap2's CPU-based KSW2 and a 7.2$\\times$ speedup over the CPU-based Edlib for long reads.","url_abs":"https://arxiv.org/abs/2203.15561v1","url_pdf":"https://arxiv.org/pdf/2203.15561v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"links_only","authors_date_abstract":"arXiv metadata, CC0 1.0 (https://info.arxiv.org/help/license), from the Kaggle arXiv metadata snapshot of 2026-09-12"},"code_links":[{"paper_slug":"algorithmic-improvement-and-gpu-acceleration","repo_url":"https://github.com/cmu-safari/scrooge","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}