Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

被引：392

作者：

Patro, Rob ^{[1
]}

Mount, Stephen M. ^{[2
,3
]}

Kingsford, Carl ^{[1
]}

机构：

[1] Carnegie Mellon Univ, Sch Comp Sci, Lane Ctr Computat Biol, Pittsburgh, PA 15213 USA

[2] Univ Maryland, Dept Cell Biol & Mol Genet, College Pk, MD 20742 USA

[3] Univ Maryland, Ctr Bioinformat & Computat Biol, College Pk, MD 20742 USA

来源：

NATURE BIOTECHNOLOGY | 2014年 / 32卷 / 05期

基金：

美国国家卫生研究院; 美国国家科学基金会;

关键词：

DIFFERENTIAL EXPRESSION; SEQUENCES;

D O I：

10.1038/nbt.2862

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

We introduce Sailfish, a computational method for quantifying the abundance of previously annotated RNA isoforms from RNA-seq data. Because Sailfish entirely avoids mapping reads, a time-consuming step in all current methods, it provides quantification estimates much faster than do existing approaches (typically 20 times faster) without loss of accuracy. By facilitating frequent reanalysis of data and reducing the need to optimize parameters, Sailfish exemplifies the potential of lightweight algorithms for efficiently processing sequencing reads.

引用

页码：462 / U174

页数：6

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