文章基本信息

标题：CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes
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作者：Marco Galardini ; Emanuele G Biondi ; Marco Bazzicalupo 等
期刊名称：Source Code for Biology and Medicine
印刷版ISSN：1751-0473
电子版ISSN：1751-0473
出版年度：2011
卷号：6
期号：1
页码：11
DOI：10.1186/1751-0473-6-11
语种：English
出版社：BioMed Central
摘要：Recent developments in sequencing technologies have given the opportunity to sequence many bacterial genomes with limited cost and labor, compared to previous techniques. However, a limiting step of genome sequencing is the finishing process, needed to infer the relative position of each contig and close sequencing gaps. An additional degree of complexity is given by bacterial species harboring more than one replicon, which are not contemplated by the currently available programs. The availability of a large number of bacterial genomes allows geneticists to use complete genomes (possibly from the same species) as templates for contigs mapping. Here we present CONTIGuator, a software tool for contigs mapping over a reference genome which allows the visualization of a map of contigs, underlining loss and/or gain of genetic elements and permitting to finish multipartite genomes. The functionality of CONTIGuator was tested using four genomes, demonstrating its improved performances compared to currently available programs. Our approach appears efficient, with a clear visualization, allowing the user to perform comparative structural genomics analysis on draft genomes. CONTIGuator is a Python script for Linux environments and can be used on normal desktop machines and can be downloaded from http://contiguator.sourceforge.net .
关键词：Genomics ; Genome finishing ; Software ; Structural genomics