使用SNAP进行更快更准确的序列比对
Faster and More Accurate Sequence Alignment with SNAP
摘要：
我们提出了可扩展的核苷酸比对程序（SNAP），这是一种新的短读段和长读段比对器，既更准确（即，对齐更多读数，错误更少），比BWA等最先进的工具快10- 100倍。与最近基于Burrows-Wheeler变换的比对器不同，SNAP使用来自基因组的短种子序列的简单散列索引，类似于BLAST。然而，SNAP通过几种措施大大减少了局部比对检查的数量和成本：它使用更长的种子来减少所考虑的假阳性位置，利用更大的内存容量来加速索引查找，并排除大多数候选位置而不完全计算其到读取的编辑距离。其结果是一种算法，该算法对于从一百到数千个碱基长的读段很好地扩展，并提供了丰富的错误模型，可以匹配突变的类别（例如，更长的插入缺失），这是今天的快速校准器所忽略的。我们计算出，SNAP可以在不到一个小时的时间内将数据集与30倍人类基因组覆盖率进行比对，在Amazon EC2上的成本为2美元，准确率高于BWA。最后，我们描述了正在进行的工作，以进一步改善SNAP。
英文摘要：
We present the Scalable Nucleotide Alignment Program (SNAP), a new short and long read aligner that is both more accurate (i.e., aligns more reads with fewer errors) and 10-100x faster than state-of-the-art tools such as BWA. Unlike recent aligners based on the Burrows-Wheeler transform, SNAP uses a simple hash index of short seed sequences from the genome, similar to BLAST's. However, SNAP greatly reduces the number and cost of local alignment checks performed through several measures: it uses longer seeds to reduce the false positive locations considered, leverages larger memory capacities to speed index lookup, and excludes most candidate locations without fully computing their edit distance to the read. The result is an algorithm that scales well for reads from one hundred to thousands of bases long and provides a rich error model that can match classes of mutations (e.g., longer indels) that today's fast aligners ignore. We calculate that SNAP can align a dataset with 30x coverage of a human genome in less than an hour for a cost of $2 on Amazon EC2, with higher accuracy than BWA. Finally, we describe ongoing work to further improve SNAP.
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。
