ABACAS: algorithm-based automatic contiguation of assembled sequences

被引：348

作者：

Assefa, Samuel ^{[1
]}

Keane, Thomas M. ^{[1
]}

Otto, Thomas D. ^{[1
]}

Newbold, Chris ^{[1
,2
]}

Berriman, Matthew ^{[1
]}

机构：

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

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

来源：

BIOINFORMATICS | 2009年 / 25卷 / 15期

基金：

英国惠康基金;

关键词：

TOOL; READS;

D O I：

10.1093/bioinformatics/btp347

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Due to the availability of new sequencing technologies, we are now increasingly interested in sequencing closely related strains of existing finished genomes. Recently a number of de novo and mapping-based assemblers have been developed to produce high quality draft genomes from new sequencing technology reads. New tools are necessary to take contigs from a draft assembly through to a fully contiguated genome sequence. ABACAS is intended as a tool to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. The input to ABACAS is a set of contigs which will be aligned to the reference genome, ordered and orientated, visualized in the ACT comparative browser, and optimal primer sequences are automatically generated.

引用

页码：1968 / 1969

页数：2

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