Minimap2: pairwise alignment for nucleotide sequences
Minimap2: pairwise alignment for nucleotide sequences
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DOI：
10.1093/bioinformatics/bty191
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发表时间：
2018-09-15
期刊：
影响因子：
5.8
通讯作者：
Li, Heng
中科院分区：
文献类型：
--
作者：
Li, Heng
动机：测序技术的最新进展有望实现平均100kb的超长阅读，高通量的全长mRNA或cdna阅读，以及长度超过100Mb的基因组重叠群。现有的比对程序无法或效率低下，无法大规模处理这些数据，这就迫切需要开发新的比对算法。结果：Minimap2是一个通用的比对程序，可以将DNA或长mRNA序列与大型参考数据库进行比对。它适用于长度为>；=100个碱基对的准确短读取，误码率类似于15%的>；=1kb基因组读出，全长杂音直接RNA或cDNA读取，以及长度为数百个百万碱基的紧密相关的全染色体。Minimap2执行拆分读对齐，对长插入和长删除使用凹陷间隙成本，并引入新的启发式算法来减少虚假对齐。在精度相当的情况下，它的速度是主流短读映射器的3-4倍，在更高的精度上，它的速度是长基因组或cDNA映射器的30倍，超过了大多数专门从事某一类型比对的对比器。
Motivation: Recent advances in sequencing technologies promise ultra-long reads of similar to 100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms.Results: Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of >= 100 bp in length, >= 1 kb genomic reads at error rate similar to 15%, full-length noisy Direct RNA or cDNA reads and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions and introduces new heuristics to reduce spurious alignments. It is 3-4 times as fast as mainstream short-read mappers at comparable accuracy, and is >= 30 times faster than longread genomic or cDNA mappers at higher accuracy, surpassing most aligners specialized in one type of alignment.