BlobToolKit - Interactive Quality Assessment of Genome Assemblies
BlobToolKit - Interactive Quality Assessment of Genome Assemblies
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DOI：
10.1534/g3.119.400908
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发表时间：
2020-04-01
影响因子：
2.6
通讯作者：
Blaxter, Mark
中科院分区：
文献类型：
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作者：
Challis, Richard;Richards, Edward;Blaxter, Mark
从不可知物种起源的仪器产生的序列数据重建靶基因组可能会受到污染DNA的干扰。无论是在样品处理过程中引入还是通过与靶DNA一起共提取引入，如果在组装过程中注意不够，最终组装的基因组可能是来自几个物种的数据的混合物。这样的组装可以混淆基于序列的生物推断，并且当存储在公共数据库中时，可能被不知道潜在问题的用户包括在下游分析中。我们提出了BlobToolKit，一个软件套件，以帮助研究人员在识别和分离非目标数据的草案和公开可用的基因组组装。BlobToolKit可用于处理汇编、读取和分析文件，以便在基于浏览器的查看器中进行完全可再现的交互式探索。BlobToolKit可在组装过程中用于过滤非靶DNA，帮助研究人员生产具有高生物可信度的组装体。我们一直在运行一个自动化的BlobToolKit管道上的真核组装公开在国际核苷酸序列数据协作，并使结果可通过公共实例的查看器。我们的目标是完成对所有公开的基因组的分析，然后保持新基因组的流动。我们努力将这些视图嵌入到欧洲核苷酸档案馆的基因组组装展示中，在公共记录旁边提供组装质量的指示，并提供链接，以便在查看器中进行全面探索。
Reconstruction of target genomes from sequence data produced by instruments that are agnostic as to the species-of-origin may be confounded by contaminant DNA. Whether introduced during sample processing or through co-extraction alongside the target DNA, if insufficient care is taken during the assembly process, the final assembled genome may be a mixture of data from several species. Such assemblies can confound sequence-based biological inference and, when deposited in public databases, may be included in downstream analyses by users unaware of underlying problems. We present BlobToolKit, a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. BlobToolKit can be used to process assembly, read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility. We have been running an automated BlobToolKit pipeline on eukaryotic assemblies publicly available in the International Nucleotide Sequence Data Collaboration and are making the results available through a public instance of the Viewer at . We aim to complete analysis of all publicly available genomes and then maintain currency with the flow of new genomes. We have worked to embed these views into the presentation of genome assemblies at the European Nucleotide Archive, providing an indication of assembly quality alongside the public record with links out to allow full exploration in the Viewer.