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| Main Authors: | , , , , |
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| Format: | Preprint |
| Published: |
2025
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2505.06127 |
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| _version_ | 1866913828688625664 |
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| author | Zhang, Zhonghai Li, Yewen Meng, Ke Zhang, Chunming Tan, Guangming |
| author_facet | Zhang, Zhonghai Li, Yewen Meng, Ke Zhang, Chunming Tan, Guangming |
| contents | 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2505_06127 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | FastDup: a scalable duplicate marking tool using speculation-and-test mechanism Zhang, Zhonghai Li, Yewen Meng, Ke Zhang, Chunming Tan, Guangming Genomics 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. |
| title | FastDup: a scalable duplicate marking tool using speculation-and-test mechanism |
| topic | Genomics |
| url | https://arxiv.org/abs/2505.06127 |