gEVAL - a web-based browser for evaluating genome assemblies

For most research approaches, genome analyses are dependent on the existence of a high quality genome reference assembly. However, the local accuracy of an assembly remains difficult to assess and improve. The gEVAL browser allows the user to interrogate an assembly in any region of the genome by co...

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Published inBioinformatics (Oxford, England) Vol. 32; no. 16; pp. 2508 - 2510
Main Authors Chow, William, Brugger, Kim, Caccamo, Mario, Sealy, Ian, Torrance, James, Howe, Kerstin
Format Journal Article
LanguageEnglish
Published England Oxford University Press 15.08.2016
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Summary:For most research approaches, genome analyses are dependent on the existence of a high quality genome reference assembly. However, the local accuracy of an assembly remains difficult to assess and improve. The gEVAL browser allows the user to interrogate an assembly in any region of the genome by comparing it to different datasets and evaluating the concordance. These analyses include: a wide variety of sequence alignments, comparative analyses of multiple genome assemblies, and consistency with optical and other physical maps. gEVAL highlights allelic variations, regions of low complexity, abnormal coverage, and potential sequence and assembly errors, and offers strategies for improvement. Although gEVAL focuses primarily on sequence integrity, it can also display arbitrary annotation including from Ensembl or TrackHub sources. We provide gEVAL web sites for many human, mouse, zebrafish and chicken assemblies to support the Genome Reference Consortium, and gEVAL is also downloadable to enable its use for any organism and assembly. Web Browser: http://geval.sanger.ac.uk, Plugin: http://wchow.github.io/wtsi-geval-plugin kj2@sanger.ac.uk Supplementary data are available at Bioinformatics online.
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Associate Editor: John Hancock
ISSN:1367-4803
1367-4811
DOI:10.1093/bioinformatics/btw159