用于BioNano数据的工具和流程：分子组装流程和FASTA超级支架工具。
Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool.
作者信息
Shelton Jennifer M, Coleman Michelle C, Herndon Nic, Lu Nanyan, Lam Ernest T, Anantharaman Thomas, Sheth Palak, Brown Susan J
机构信息
KSU/K-INBRE Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS, USA.
BioNano Genomics, San Diego, CA, USA.
出版信息
BMC Genomics. 2015 Sep 29;16:734. doi: 10.1186/s12864-015-1911-8.
BACKGROUND
Genome assembly remains an unsolved problem. Assembly projects face a range of hurdles that confound assembly. Thus a variety of tools and approaches are needed to improve draft genomes.
RESULTS
We used a custom assembly workflow to optimize consensus genome map assembly, resulting in an assembly equal to the estimated length of the Tribolium castaneum genome and with an N50 of more than 1 Mb. We used this map for super scaffolding the T. castaneum sequence assembly, more than tripling its N50 with the program Stitch.
CONCLUSIONS
In this article we present software that leverages consensus genome maps assembled from extremely long single molecule maps to increase the contiguity of sequence assemblies. We report the results of applying these tools to validate and improve a 7x Sanger draft of the T. castaneum genome.
背景
基因组组装仍然是一个未解决的问题。组装项目面临一系列阻碍组装的难题。因此，需要各种工具和方法来改进基因组草图。
结果
我们使用了一个定制的组装工作流程来优化一致性基因组图谱组装，得到了一个长度与赤拟谷盗基因组估计长度相当、N50超过1 Mb的组装结果。我们使用这个图谱对赤拟谷盗序列组装进行超级支架构建，通过Stitch程序使其N50增加了两倍多。
结论
在本文中，我们展示了利用从极长单分子图谱组装得到的一致性基因组图谱来提高序列组装连续性的软件。我们报告了将这些工具应用于验证和改进赤拟谷盗基因组7倍覆盖率的桑格测序草图的结果。
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