{"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/fastdup-a-scalable-duplicate-marking-tool","title":"FastDup: a scalable duplicate marking tool using speculation-and-test mechanism","arxiv_id":"2505.06127","date":"2025-05-09","proceeding":null,"authors":["Zhonghai Zhang","Yewen Li","Ke Meng","Chunming Zhang","Guangming Tan"],"abstract":"Duplicate marking is a critical preprocessing step in gene sequence analysis to flag redundant reads arising from polymerase chain reaction(PCR) amplification and sequencing artifacts. Although Picard MarkDuplicates is widely recognized as the gold-standard tool, its single-threaded implementation and reliance on global sorting result in significant computational and resource overhead, limiting its efficiency on large-scale datasets. Here, we introduce FastDup: a high-performance, scalable solution that follows the speculation-and-test mechanism. FastDup achieves up to 20x throughput speedup and guarantees 100\\% identical output compared to Picard MarkDuplicates. FastDup is a C++ program available from GitHub (https://github.com/zzhofict/FastDup.git) under the MIT license.","url_abs":"https://arxiv.org/abs/2505.06127v1","url_pdf":"https://arxiv.org/pdf/2505.06127v1.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":"abstracts"},"code_links":[{"paper_slug":"fastdup-a-scalable-duplicate-marking-tool","repo_url":"https://github.com/zzhofict/fastdup","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[{"method_slug":"picard","method_name":"PICARD"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}