发表机构
Technical University of Denmark（丹麦技术大学）
机构由 AI 辅助整理，请以论文原文为准。AI 中文总结
PlainMap是一个轻量级、可重启的比对流程，支持现代和降解DNA，通过确定性分块和检查点机制实现中断恢复，并减少约25%峰值内存。
AI 中文摘要
将测序读段比对到参考基因组需要预处理和比对选择，这些选择可能因文库类型、片段长度、测序平台和参考基因组而异。这些考虑因素对于古代和历史DNA尤为重要，因为短且受损的片段可能使得最合适的比对策略难以事先确定。我们提出了PlainMap，一个用于现代和降解DNA测序数据的轻量级、可重启的比对流程。PlainMap接受简单的FASTQ文件清单，自动从读段头识别单端和双端数据，支持混合测序平台，并为现代和降解DNA提供替代比对策略。确定性的分块和基于检查点的执行允许大型分析在中断后恢复，而可选的试点子采样使得能够使用相同的原始片段子集对比对策略进行经验比较。PlainMap生成重复过滤的BAM文件以及片段感知的比对和覆盖度统计。使用异质测序数据的评估确认了三种比对模式的预期行为，而自适应分块将峰值内存使用减少了约25%，并允许中断的分析从已完成的比对块恢复。PlainMap实现为单个Bash脚本，可在https://github.com/BiodiversityExtinction/PlainMap免费获取。
英文摘要
Mapping sequencing reads to a reference genome requires preprocessing and alignment choices that can vary with library type, fragment length, sequencing platform, and reference genome. These considerations are particularly important for ancient and historical DNA, where short and damaged fragments can make the most appropriate mapping strategy difficult to determine a priori. We present PlainMap, a lightweight and restartable mapping pipeline for modern and degraded DNA sequencing data. PlainMap accepts a simple manifest of FASTQ files, automatically identifies single-end and paired-end data from read headers, supports mixed sequencing platforms, and provides alternative mapping strategies for modern and degraded DNA. Deterministic chunking and checkpoint-based execution allow large analyses to resume after interruption, while optional pilot subsampling enables empirical comparison of mapping strategies using identical subsets of raw fragments. PlainMap produces duplicate-filtered BAM files together with fragment-aware mapping and coverage statistics. Evaluation using heterogeneous sequencing data confirmed the expected behaviour of the three mapping modes, while adaptive chunking reduced peak memory use by approximately 25% and allowed an interrupted analysis to resume from completed mapping chunks. PlainMap is implemented as a single Bash script and is freely available at https://github.com/BiodiversityExtinction/PlainMap.
