biobambam：基于BAM文件算法的读段对排序工具
biobambam: tools for read pair collation based algorithms on BAM files
摘要：
当存储在BAM文件中时，序列比对数据通常按坐标（参考序列的id加上片段被映射的序列上的位置）排序，因为这简化了映射数据和参考之间的变体或映射数据内的变体的提取。按照这种顺序，配对读段通常在文件中分开，这使得一些其他应用复杂化，例如重复标记或转换为FastQ格式，这些应用需要访问配对的全部信息。在本文中，我们介绍biobambam，一个API的高效BAM文件读取支持有效整理的路线读名称，而不执行一个完整的重新排序的输入文件和一些工具，基于这个API执行的任务，如标记重复读取和转换为FastQ格式。与以前的方法相比，涉及通过读段名称整理比对的问题，如BAM到FastQ或Picard套件中的重复标记实用程序，biobambam的方法通常可以在所需的主内存和运行时间方面更有效地执行等效任务。
英文摘要：
Sequence alignment data is often ordered by coordinate (id of the reference sequence plus position on the sequence where the fragment was mapped) when stored in BAM files, as this simplifies the extraction of variants between the mapped data and the reference or of variants within the mapped data. In this order paired reads are usually separated in the file, which complicates some other applications like duplicate marking or conversion to the FastQ format which require to access the full information of the pairs. In this paper we introduce biobambam, an API for efficient BAM file reading supporting the efficient collation of alignments by read name without performing a complete resorting of the input file and some tools based on this API performing tasks like marking duplicate reads and conversion to the FastQ format. In comparison with previous approaches to problems involving the collation of alignments by read name like the BAM to FastQ or duplication marking utilities in the Picard suite the approach of biobambam can often perform an equivalent task more efficiently in terms of the required main memory and run-time.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
