2025/05/09 by Zhonghai Zhang, Zhang, Zhonghai, Yewen Li +7 · 1 voice
Biochemistry, Genetics and Molecular Biology · Chemistry · Computer Science · #Advanced Proteomics Techniques and Applications #FOS: Biological sciences #Genomics (q-bio.GN) #Genomics and Phylogenetic Studies #Software Testing and Debugging Techniques #q-bio.GN
paper · pdf · doi:10.48550/arxiv.2505.06127
openalex publication_date 2025/05/09 · arxiv published 2025/05/09 · arxiv updated 2025/05/09 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.