Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology

被引：162

作者：

Otto, Thomas D. ^{[1
]}

Sanders, Mandy ^{[1
]}

Berriman, Matthew ^{[1
]}

Newbold, Chris ^{[1
,2
]}

机构：

[1] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[2] Univ Oxford, John Radcliffe Hosp, Weatherall Inst Mol Med, Oxford OX3 9DS, England

来源：

BIOINFORMATICS | 2010年 / 26卷 / 14期

基金：

英国惠康基金;

关键词：

GENOME; SYSTEM;

D O I：

10.1093/bioinformatics/btq269

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: The accuracy of reference genomes is important for downstream analysis but a low error rate requires expensive manual interrogation of the sequence. Here, we describe a novel algorithm (Iterative Correction of Reference Nucleotides) that iteratively aligns deep coverage of short sequencing reads to correct errors in reference genome sequences and evaluate their accuracy. Results: Using Plasmodium falciparum (81% A + T content) as an extreme example, we show that the algorithm is highly accurate and corrects over 2000 errors in the reference sequence. We give examples of its application to numerous other eukaryotic and prokaryotic genomes and suggest additional applications.

引用

页码：1704 / 1707

页数：4

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