Efficient mapping of accurate long reads in minimizer space with mapquik.
Efficient mapping of accurate long reads in minimizer space with mapquik.
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DOI：
10.1101/gr.277679.123
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发表时间：
2023-07
期刊：
影响因子：
7
通讯作者：
Chikhi, Rayan
中科院分区：
文献类型：
--
作者：
Ekim, Baris;Sahlin, Kristoffer;Medvedev, Paul;Berger, Bonnie;Chikhi, Rayan
DNA测序数据继续朝着更长的读数发展，测序错误率越来越低。我们专注于映射或比对来自长读段的低趋异序列的关键问题（例如，Pacific Biosciences [PacBio] HiFi）与参考基因组进行比对，这在使用专为所有类型比对设计的尖端读段作图方法时，在准确性和计算资源方面提出了挑战。一个自然的想法是使用较长的种子来优化效率，以减少无关匹配的概率;然而，连续的精确种子很快就会达到灵敏度极限。我们介绍mapquik，一种新的策略，通过锚定比对，通过匹配k连续采样的最小值（-最小-聚体），只有索引-最小-聚体，在参考基因组中发生一次，从而解锁超快映射，同时保持高灵敏度，从而创建准确的较长的种子。我们发现mapquik显著加速了播种和链接步骤读取图谱的基本瓶颈对于人类和玉米基因组都具有灵敏度和近乎完美的特异性。在人类基因组上，无论是真实的还是模拟的读取，mapquik都比最先进的工具minimap2实现了更快的速度，在玉米基因组上，mapquik也比minimap2实现了更快的速度，使mapquik成为迄今为止最快的映射器。这些加速不仅可以从最小化空间播种，而且还可以从一种新的启发式伪链算法，该算法改进了长期存在的边界。最小化空间计算为实现长读序测序数据的实时分析奠定了基础。
DNA sequencing data continue to progress toward longer reads with increasingly lower sequencing error rates. We focus on the critical problem of mapping, or aligning, low-divergence sequences from long reads (e.g., Pacific Biosciences [PacBio] HiFi) to a reference genome, which poses challenges in terms of accuracy and computational resources when using cutting-edge read mapping approaches that are designed for all types of alignments. A natural idea would be to optimize efficiency with longer seeds to reduce the probability of extraneous matches; however, contiguous exact seeds quickly reach a sensitivity limit. We introduce mapquik, a novel strategy that creates accurate longer seeds by anchoring alignments through matches of k consecutively sampled minimizers (-min-mers) and only indexing -min-mers that occur once in the reference genome, thereby unlocking ultrafast mapping while retaining high sensitivity. We show that mapquik significantly accelerates the seeding and chaining steps—fundamental bottlenecks to read mapping—for both the human and maize genomes with sensitivity and near-perfect specificity. On the human genome, for both real and simulated reads, mapquik achieves a speedup over the state-of-the-art tool minimap2, and on the maize genome, mapquik achieves a speedup over minimap2, making mapquik the fastest mapper to date. These accelerations are enabled from not only minimizer-space seeding but also a novel heuristic pseudochaining algorithm, which improves upon the long-standing bound. Minimizer-space computation builds the foundation for achieving real-time analysis of long-read sequencing data.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng
DOI：
10.1038/s41576-020-0236-x
发表时间：
2020-10
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
Logsdon GA;Vollger MR;Eichler EE
通讯作者：
Eichler EE
影响因子：
46.9
作者：
Kolmogorov, Mikhail;Yuan, Jeffrey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.
影响因子：
14.9
作者：
Li, Wenjun;O'Neill, Kathleen R.;Thibaud-Nissen, Francoise
通讯作者：
Thibaud-Nissen, Francoise