Pan-genomic matching statistics for targeted nanopore sequencing.
Pan-genomic matching statistics for targeted nanopore sequencing.
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DOI：
10.1016/j.isci.2021.102696
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发表时间：
2021-06-25
期刊：
影响因子：
5.8
通讯作者：
Langmead B
中科院分区：
文献类型：
--
作者：
Ahmed O;Rossi M;Kovaka S;Schatz MC;Gagie T;Boucher C;Langmead B
纳米孔测序是基因组学日益强大的工具。最近，计算的进步已经允许纳米孔以靶向方式进行测序;当测序仪发出数据时，软件可以真实的分析数据，并向测序仪发出信号以排出“非靶”DNA分子。我们提出了一种称为SPUMONI的新方法，该方法可以使用有效的泛基因组索引进行快速准确的靶向测序。SPUMONI使用压缩索引以流式方式快速生成精确或近似的匹配统计数据。当用于靶向模拟社区中的特定菌株时，SPUMONI具有与minimap 2相似的准确性，当两者都针对每个物种包含许多菌株的索引运行时。SPUMONI比minimap 2快12倍。SPUMONI的索引和峰值内存占用也分别比minimap 2小16到4倍。这可以实现精确的靶向测序，即使当靶向菌株之前不一定被测序或组装时。SPUMONI使用有效的泛基因组索引从纳米孔中弹出非靶读段读段分类对于典型的纳米孔测序错误率非常准确对于较大的泛基因组，SPUMONI比minimap更快，使用的内存更少2能够分析数据库中缺失或代表性差的菌株基因组学;生物技术;生物信息学;生物计算方法
Nanopore sequencing is an increasingly powerful tool for genomics. Recently, computational advances have allowed nanopores to sequence in a targeted fashion; as the sequencer emits data, software can analyze the data in real time and signal the sequencer to eject “nontarget” DNA molecules. We present a novel method called SPUMONI, which enables rapid and accurate targeted sequencing using efficient pan-genome indexes. SPUMONI uses a compressed index to rapidly generate exact or approximate matching statistics in a streaming fashion. When used to target a specific strain in a mock community, SPUMONI has similar accuracy as minimap2 when both are run against an index containing many strains per species. However SPUMONI is 12 times faster than minimap2. SPUMONI's index and peak memory footprint are also 16 to 4 times smaller than those of minimap2, respectively. This could enable accurate targeted sequencing even when the targeted strains have not necessarily been sequenced or assembled previously. SPUMONI uses an efficient pan-genome index to eject nontarget reads from the nanopore Read classifications are highly accurate for typical nanopore sequencing error rates For larger pan-genomes, SPUMONI is faster and uses less memory than minimap2 Enables analyses for strains that are missing or poorly represented in databases Genomics; Biotechnology; Bioinformatics; Biocomputational method
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