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

Yuxuan Yuan,Armin Scheben,David Edwards,Philipp E Bayer,Chon-Kit Kenneth Chan

doi:10.1186/s12859-017-1735-4

Yuxuan Yuan, Armin Scheben + Show 3 more

Open Access

https://doi.org/10.1186/s12859-017-1735-4

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Journal: BMC Bioinformatics	Publication Date: Jun 30, 2017
Citations: 9	License type: open-access

Affiliation: University of Western Australia

Abstract

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.

Highlights

Reference genome assemblies are valuable, as they provide insights into gene content, genetic evolution and domestication
All information is displayed by clicking the respective button on the “Workflow” canvas (Fig. 3a)
The GFF3 file generated by BioNanoAnalyst can be imported directly to a genome browser such as JBrowse [14], to visualise the location and nucleotide sequences of the predicted misassemblies (Fig. 4b)

Summary

Introduction

Reference genome assemblies are valuable, as they provide insights into gene content, genetic evolution and domestication. Due to the large number of repetitive regions in some genomes and the short length of sequencing reads, assemblies generated using SGS are often collapsed and fragmented [2]. The most common optical mapping approach uses the BioNano Irys and has been applied to a wide range of organisms [6,7,8,9,10,11] Among these studies, most used BioNano optical mapping to help genome scaffolding and for structural variation detection, and there are still no studies reported of genome misassembly identification and correction using BioNano data or use of this data to examine the reference genome assembly quality.

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Discussion

Conclusion