Accurate detection of chimeric contigs via Bionano optical maps
Accurate detection of chimeric contigs via Bionano optical maps
复制标题
DOI：
10.1093/bioinformatics/bty850
复制
发表时间：
2019-05-15
期刊：
影响因子：
5.8
通讯作者：
Lonardi, Stefano
中科院分区：
文献类型：
--
作者：
Pan, Weihua;Lonardi, Stefano
嵌合重叠群是被错误组装的重叠群，即包含一个或多个错误连接的重叠群。嵌合重叠群的检测可以通过将组装的重叠群与全基因组图谱（例如遗传、物理或光学图谱）比对或通过将测序读数映射到组装的重叠群来进行。在这里，我们介绍了一种名为 Chimericognizer 的软件工具，它利用一个或多个 Bionano Genomics 光学图谱来准确检测和纠正嵌合重叠群。实验结果表明 Chimericognizer 非常准确，并且明显优于 Bionano Hybrid Scaffold pipeline 提供的嵌合检测方法。 Chimericognizer还可以检测和校正嵌合光学分子。可用性和实现https://github.com/ucrbioinfo/Chimericognizer补充信息补充数据可在生物信息学在线获取。
A chimeric contig is contig that has been incorrectly assembled, i.e. a contig that contains one or more mis-joins. The detection of chimeric contigs can be carried out either by aligning assembled contigs to genome-wide maps (e.g. genetic, physical or optical maps) or by mapping sequenced reads to the assembled contigs. Here, we introduce a software tool called Chimericognizer that takes advantage of one or more Bionano Genomics optical maps to accurately detect and correct chimeric contigs. Experimental results show that Chimericognizer is very accurate, and significantly better than the chimeric detection method offered by the Bionano Hybrid Scaffold pipeline. Chimericognizer can also detect and correct chimeric optical molecules.Availability and implementationhttps://github.com/ucrbioinfo/ChimericognizerSupplementary informationSupplementary data are available at Bioinformatics online.