串联工具：长读映射和评估/改进超长串联重复序列的组装质量。
TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats.
机构信息
Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg 199034, Russia.
Graduate Program in Bioinformatics and Systems Biology, University of California, San Diego, CA 92093, USA.
出版信息
Bioinformatics. 2020 Jul 1;36(Suppl_1):i75-i83. doi: 10.1093/bioinformatics/btaa440.
MOTIVATION
Extra-long tandem repeats (ETRs) are widespread in eukaryotic genomes and play an important role in fundamental cellular processes, such as chromosome segregation. Although emerging long-read technologies have enabled ETR assemblies, the accuracy of such assemblies is difficult to evaluate since there are no tools for their quality assessment. Moreover, since the mapping of error-prone reads to ETRs remains an open problem, it is not clear how to polish draft ETR assemblies.
RESULTS
To address these problems, we developed the TandemTools software that includes the TandemMapper tool for mapping reads to ETRs and the TandemQUAST tool for polishing ETR assemblies and their quality assessment. We demonstrate that TandemTools not only reveals errors in ETR assemblies but also improves the recently generated assemblies of human centromeres.
AVAILABILITY AND IMPLEMENTATION
https://github.com/ablab/TandemTools.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机
串联重复（ETR）广泛存在于真核生物基因组中，在诸如染色体分离等基本细胞过程中发挥着重要作用。尽管新兴的长读长技术已经能够进行 ETR 组装，但由于缺乏针对其质量评估的工具，此类组装的准确性难以评估。此外，由于易错读序列向 ETR 映射仍然是一个悬而未决的问题，因此尚不清楚如何优化 ETR 组装的草案。
结果
为了解决这些问题，我们开发了 TandemTools 软件，其中包括用于将读序列映射到 ETR 的 TandemMapper 工具和用于优化 ETR 组装及其质量评估的 TandemQUAST 工具。我们证明，TandemTools 不仅能够揭示 ETR 组装中的错误，还能改进最近生成的人类着丝粒组装。
可用性和实现
https://github.com/ablab/TandemTools。
补充信息
补充数据可在“Bioinformatics”在线获取。
Zotero 插件