Meta比对器：基于基因组统计信息的长读段比对。
Meta-aligner: long-read alignment based on genome statistics.
作者信息
Nashta-Ali Damoon, Aliyari Ali, Ahmadian Moghadam Ahmad, Edrisi Mohammad Amin, Motahari Seyed Abolfazl, Hossein Khalaj Babak
机构信息
Department of Electrical Engineering, Sharif University of Technology, Tehran, Azadi, Iran.
Department of Computer Engineering, Sharif University of Technology, Azadi, Tehran, Iran.
出版信息
BMC Bioinformatics. 2017 Feb 23;18(1):126. doi: 10.1186/s12859-017-1518-y.
BACKGROUND
Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment of these reads play an important role in any downstream analysis. Similarly, reducing the overall cost of sequencing is related to the time consumption of the aligner. The tradeoff between accuracy and speed is the main challenge in designing long read aligners.
RESULTS
We propose Meta-aligner which aligns long and very long reads to the reference genome very efficiently and accurately. Meta-aligner incorporates available short/long aligners as subcomponents and uses statistics from the reference genome to increase the performance. Meta-aligner estimates statistics from reads and the reference genome automatically. Meta-aligner is implemented in C++ and runs in popular POSIX-like operating systems such as Linux.
CONCLUSIONS
Meta-aligner achieves high recall rates and precisions especially for long reads and high error rates. Also, it improves performance of alignment in the case of PacBio long-reads in comparison with traditional schemes.
背景
目前测序技术的发展趋势是生成更长且噪声更大的 reads。显然，这些 reads 的精确比对在任何下游分析中都起着重要作用。同样，降低测序的总体成本与比对器的时间消耗相关。准确性和速度之间的权衡是设计长 reads 比对器的主要挑战。
结果
我们提出了 Meta-aligner，它能非常高效且准确地将长 reads 和非常长的 reads 与参考基因组进行比对。Meta-aligner 将可用的短/长比对器作为子组件，并利用参考基因组的统计信息来提高性能。Meta-aligner 会自动从 reads 和参考基因组中估计统计信息。Meta-aligner 用 C++ 实现，可在流行的类 POSIX 操作系统（如 Linux）上运行。
结论
Meta-aligner 尤其在长 reads 和高错误率的情况下实现了高召回率和高精度。此外，与传统方案相比，它在 PacBio 长 reads 的情况下提高了比对性能。
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