太碱基规模的BWT构建与搜索
BWT construction and search at the terabase scale
AI总结：
本文提出ropebwt3工具，实现太碱基规模下高效BWT构建与查询，支持精确匹配、非精确比对及局部单倍型检索，证明了全文本索引在超大基因组数据上的可行性。
摘要：
动机：Burrows-Wheeler变换（BWT）是全文本索引中的常见组件。它最初为数据压缩而开发，在编码冗余序列（如泛基因组数据）方面特别强大。然而，BWT构建资源密集且难以并行化，而且许多查询大型全文本索引的方法仅报告精确匹配或其简单扩展。这些限制阻碍了全文本索引在生物学中的应用。结果：我们开发了ropebwt3，用于高效的BWT构建和查询。Ropebwt3在65小时内索引了320个人类基因组，并在26天内索引了7.3太碱基的常见细菌组装序列。这在使用峰值170吉字节内存且无需工作磁盘空间的情况下实现。Ropebwt3可以找到最大精确匹配和仿射缺口罚分下的非精确比对，并能检索与查询序列相似的局部单倍型。它证明了在太碱基规模下进行全文本索引的可行性。可用性和实现：https://github.com/lh3/ropebwt3
英文摘要：
Motivation: Burrows-Wheeler Transform (BWT) is a common component in full-text indices. Initially developed for data compression, it is particularly powerful for encoding redundant sequences such as pangenome data. However, BWT construction is resource intensive and hard to be parallelized, and many methods for querying large full-text indices only report exact matches or their simple extensions. These limitations have hampered the biological applications of full-text indices. Results: We developed ropebwt3 for efficient BWT construction and query. Ropebwt3 indexed 320 assembled human genomes in 65 hours and indexed 7.3 terabases of commonly studied bacterial assemblies in 26 days. This was achieved using up to 170 gigabytes of memory at the peak without working disk space. Ropebwt3 can find maximal exact matches and inexact alignments under affine-gap penalties, and can retrieve similar local haplotypes matching a query sequence. It demonstrates the feasibility of full-text indexing at the terabase scale. Availability and implementation: https://github.com/lh3/ropebwt3
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。
