Simulation-based comprehensive benchmarking of RNA-seq aligners

被引：0

作者：

Baruzzo, Giacomo ^{[1
]}

Hayer, Katharina E. ^{[2
]}

Kim, Eun Ji ^{[2
]}

Di Camillo, Barbara ^{[1
]}

FitzGerald, Garret A. ^{[2
,3
]}

Grant, Gregory R. ^{[2
,4
]}

机构：

[1] Univ Padua, Dept Informat Engn, Padua, Italy

[2] Univ Penn, Inst Translat Med & Therapeut, Philadelphia, PA 19104 USA

[3] Univ Penn, Dept Syst Pharmacol & Translat Therapeut, Philadelphia, PA 19104 USA

[4] Univ Penn, Dept Genet, Philadelphia, PA 19104 USA

来源：

NATURE METHODS | 2017年 / 14卷 / 02期

关键词：

ACCURATE; ALIGNMENT; READS;

D O I：

10.1038/NMETH.4106

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Alignment is the first step in most RNA-seq analysis pipelines, and the accuracy of downstream analyses depends heavily on it. Unlike most steps in the pipeline, alignment is particularly amenable to benchmarking with simulated data. We performed a comprehensive benchmarking of 14 common splice-aware aligners for base, read, and exon junction-level accuracy and compared default with optimized parameters. We found that performance varied by genome complexity, and accuracy and popularity were poorly correlated. The most widely cited tool underperforms for most metrics, particularly when using default settings.

引用

页码：135 / 139

页数：5

共 19 条

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