SGTK：一个支架图可视化和评估的工具包。
SGTK: a toolkit for visualization and assessment of scaffold graphs.
机构信息
Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia.
出版信息
Bioinformatics. 2019 Jul 1;35(13):2303-2305. doi: 10.1093/bioinformatics/bty956.
SUMMARY
Scaffolding is an important step in every genome assembly pipeline, which allows to order contigs into longer sequences using various types of linkage information, such as mate-pair libraries and long reads. In this work, we operate with a notion of a scaffold graph-a graph, vertices of which correspond to the assembled contigs and edges represent connections between them. We present a software package called Scaffold Graph ToolKit that allows to construct and visualize scaffold graphs using different kinds of sequencing data. We show that the scaffold graph appears to be useful for analyzing and assessing genome assemblies, and demonstrate several use cases that can be helpful for both assembly software developers and their users.
AVAILABILITY AND IMPLEMENTATION
SGTK is implemented in C++, Python and JavaScript and is freely available at https://github.com/olga24912/SGTK.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
支架是每个基因组组装管道中的一个重要步骤，它允许使用各种类型的链接信息（如 mate-pair 文库和长读段）将 contigs 排列成长序列。在这项工作中，我们使用支架图的概念——一个图，其顶点对应于组装的 contigs，边表示它们之间的连接。我们展示了一个名为 Scaffold Graph ToolKit 的软件包，它允许使用不同类型的测序数据构建和可视化支架图。我们表明，支架图对于分析和评估基因组组装是有用的，并展示了几个用例，这些用例对组装软件的开发人员及其用户都有帮助。
可用性和实现
SGTK 是用 C++、Python 和 JavaScript 实现的，可在 https://github.com/olga24912/SGTK 上免费获得。
补充信息
补充数据可在 Bioinformatics 在线获得。
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