BioNanoAnalyst: a visualisation tool to assess genome assembly quality using BioNano data
Abstract Background Reference 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 m...
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doaj-b91450b1ddaa49598b5db8458125646a2020-11-24T22:17:22ZengBMCBMC Bioinformatics1471-21052017-06-011811910.1186/s12859-017-1735-4BioNanoAnalyst: a visualisation tool to assess genome assembly quality using BioNano dataYuxuan Yuan0Philipp E. Bayer1Armin Scheben2Chon-Kit Kenneth Chan3David Edwards4School of Biological Sciences, the University of Western AustraliaSchool of Biological Sciences, the University of Western AustraliaSchool of Biological Sciences, the University of Western AustraliaSchool of Biological Sciences, the University of Western AustraliaSchool of Biological Sciences, the University of Western AustraliaAbstract Background Reference 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. Results We 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. Conclusions BioNanoAnalyst 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.http://link.springer.com/article/10.1186/s12859-017-1735-4BioNanoMisassemblyRestriction enzyme cut siteOptical map |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Yuxuan Yuan Philipp E. Bayer Armin Scheben Chon-Kit Kenneth Chan David Edwards |
spellingShingle |
Yuxuan Yuan Philipp E. Bayer Armin Scheben Chon-Kit Kenneth Chan David Edwards BioNanoAnalyst: a visualisation tool to assess genome assembly quality using BioNano data BMC Bioinformatics BioNano Misassembly Restriction enzyme cut site Optical map |
author_facet |
Yuxuan Yuan Philipp E. Bayer Armin Scheben Chon-Kit Kenneth Chan David Edwards |
author_sort |
Yuxuan Yuan |
title |
BioNanoAnalyst: a visualisation tool to assess genome assembly quality using BioNano data |
title_short |
BioNanoAnalyst: a visualisation tool to assess genome assembly quality using BioNano data |
title_full |
BioNanoAnalyst: a visualisation tool to assess genome assembly quality using BioNano data |
title_fullStr |
BioNanoAnalyst: a visualisation tool to assess genome assembly quality using BioNano data |
title_full_unstemmed |
BioNanoAnalyst: a visualisation tool to assess genome assembly quality using BioNano data |
title_sort |
bionanoanalyst: a visualisation tool to assess genome assembly quality using bionano data |
publisher |
BMC |
series |
BMC Bioinformatics |
issn |
1471-2105 |
publishDate |
2017-06-01 |
description |
Abstract Background Reference 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. Results We 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. Conclusions BioNanoAnalyst 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. |
topic |
BioNano Misassembly Restriction enzyme cut site Optical map |
url |
http://link.springer.com/article/10.1186/s12859-017-1735-4 |
work_keys_str_mv |
AT yuxuanyuan bionanoanalystavisualisationtooltoassessgenomeassemblyqualityusingbionanodata AT philippebayer bionanoanalystavisualisationtooltoassessgenomeassemblyqualityusingbionanodata AT arminscheben bionanoanalystavisualisationtooltoassessgenomeassemblyqualityusingbionanodata AT chonkitkennethchan bionanoanalystavisualisationtooltoassessgenomeassemblyqualityusingbionanodata AT davidedwards bionanoanalystavisualisationtooltoassessgenomeassemblyqualityusingbionanodata |
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1725785067932876800 |