BioNanoAnalyst: a visualisation tool to assess genome assembly quality using BioNano data

BMC Bioinformatics

Software

Armin Scheben¹  Philipp E. Bayer¹  Chon-Kit Kenneth Chan¹  Yuxuan Yuan¹  David Edwards¹ 

[1] School of Biological Sciences, the University of Western Australia, Perth, WA, Australia;

关键词: BioNano;    Misassembly;    Restriction enzyme cut site;    Optical map;   

DOI  :  10.1186/s12859-017-1735-4

 received in 2017-03-08, accepted in 2017-06-20,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundReference genome assemblies are valuable, as they provide insights into gene content, genetic evolution and domestication. The higher the quality of a reference genome assembly the more accurate the downstream analysis will be. During the last few years, major efforts have been made towards improving the quality of genome assemblies. However, erroneous and incomplete assemblies are still common. Complementary to DNA sequencing technologies, optical mapping has advanced genomic studies by facilitating the production of genome scaffolds and assessing structural variation. However, there are few tools available to comprehensively examine misassemblies in reference genome sequences using optical map data.ResultsWe present BioNanoAnalyst, a software package to examine genome assemblies based on restriction endonuclease cut sites and optical map data. A graphical user interface (GUI) allows users to assess reference genome sequences on different computer platforms without the requirement of programming knowledge. The zoom function makes visualisation convenient, while a GFF3 format output file gives an option to directly visualise questionable assembly regions by location and nucleotides following import into a local genome browser.ConclusionsBioNanoAnalyst is a tool to identify misassemblies in a reference genome sequence using optical map data. With the reported information, users can rapidly identify assembly errors and correct them using other software tools, which could facilitate an accurate downstream analysis.

【 授权许可】

CC BY   
© The Author(s). 2017