Gap5-editing the billion fragment sequence assembly

被引：151

作者：

Bonfield, James K. ^{[1
]}

Whitwham, Andrew ^{[1
]}

机构：

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

来源：

BIOINFORMATICS | 2010年 / 26卷 / 14期

基金：

英国医学研究理事会; 英国惠康基金;

关键词：

GENOME; TOOL;

D O I：

10.1093/bioinformatics/btq268

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: Existing sequence assembly editors struggle with the volumes of data now readily available from the latest generation of DNA sequencing instruments. Results: We describe the Gap5 software along with the data structures and algorithms used that allow it to be scalable. We demonstrate this with an assembly of 1.1 billion sequence fragments and compare the performance with several other programs. We analyse the memory, CPU, I/O usage and file sizes used by Gap5.

引用

页码：1699 / 1703

页数：5

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