BACCardI -: a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison
BACCardI -: a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison
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DOI：
10.1093/bioinformatics/bti091
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发表时间：
2005-04-01
期刊：
影响因子：
5.8
通讯作者：
Schuster, SC
中科院分区：
文献类型：
--
作者：
Bartels, D;Kespohl, S;Schuster, SC
总结：我们提供了图形工具BACCardI，用于从标准汇编程序输出文件或基于BLAST的序列比较构建虚拟克隆图。这种新工具已应用于许多基因组计划，以解决各种问题，包括（a）全基因组鸟枪组装的验证，（B）在基因组计划的完成阶段支持重叠群排序，以及（c）当只有一个菌株被测序而另一个菌株有大的插入文库时，相关菌株之间的基因组间比较。BACCardI软件可以与各种序列组装包无缝交互。动机：由序列信息生成的基因组组装需要通过独立的方法（如物理图谱）进行验证。构建物理映射的耗时任务可以通过从大型插入库的读对信息导出的虚拟克隆映射来规避。
Summary: We provide the graphical tool BACCardI for the construction of virtual clone maps from standard assembler output files or BLAST based sequence comparisons. This new tool has been applied to numerous genome projects to solve various problems including (a) validation of whole genome shotgun assemblies, (b) support for contig ordering in the finishing phase of a genome project, and (c) intergenome comparison between related strains when only one of the strains has been sequenced and a large insert library is available for the other. The BACCardI software can seamlessly interact with various sequence assembly packages.Motivation: Genomic assemblies generated from sequence information need to be validated by independent methods such as physical maps. The time-consuming task of building physical maps can be circumvented by virtual clone maps derived from read pair information of large insert libraries.