HISAT: a fast spliced aligner with low memory requirements.
HISAT: a fast spliced aligner with low memory requirements.
复制标题
DOI：
10.1038/nmeth.3317
复制
发表时间：
2015-04
期刊：
影响因子：
48
通讯作者：
Salzberg SL
中科院分区：
文献类型：
--
作者：
Kim D;Langmead B;Salzberg SL
HISAT（hierarchical indexing for spliced alignment of transcripts）是一种用于比对RNA测序实验中的读段的高效系统。HISAT使用基于Burrows-Wheeler变换和Ferragina-Manzini（FM）索引的索引方案，采用两种类型的索引进行比对：用于锚每个比对的全基因组FM索引和用于这些比对的非常快速的扩展的许多局部FM索引。HISAT的人类基因组分层索引包含48，000个局部FM索引，每个索引代表约64，000 bp的基因组区域。对真实的和模拟数据集的测试表明，HISAT是目前可用的最快的系统，具有与任何其他方法相同或更好的准确性。尽管有大量的索引，HISAT只需要4.3千兆字节的内存。HISAT支持任何大小的基因组，包括大于40亿个碱基的基因组。
HISAT (hierarchical indexing for spliced alignment of transcripts) is a highly efficient system for aligning reads from RNA sequencing experiments. HISAT uses an indexing scheme based on the Burrows-Wheeler transform and the Ferragina-Manzini (FM) index, employing two types of indexes for alignment: a whole-genome FM index to anchor each alignment and numerous local FM indexes for very rapid extensions of these alignments. HISAT’s hierarchical index for the human genome contains 48,000 local FM indexes, each representing a genomic region of ~64,000 bp. Tests on real and simulated data sets showed that HISAT is the fastest system currently available, with equal or better accuracy than any other method. Despite its large number of indexes, HISAT requires only 4.3 gigabytes of memory. HISAT supports genomes of any size, including those larger than 4 billion bases.