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 in | Bioinformatics (Oxford, England) Vol. 32; no. 16; pp. 2508 - 2510 |
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| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
15.08.2016
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| Subjects | |
| Online Access | Get full text |
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| Abstract | 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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| AbstractList | Motivation: 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.
Availability and Implementation: Web Browser: http://geval.sanger.ac.uk, Plugin: http://wchow.github.io/wtsi-geval-plugin.
Contact: kj2@sanger.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online. 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. Motivation: 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. Availability and Implementation: Web Browser: http://geval.sanger.ac.uk , Plugin: http://wchow.github.io/wtsi-geval-plugin . Contact: kj2@sanger.ac.uk Supplementary information : Supplementary data are available at Bioinformatics online. MOTIVATIONFor 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.AVAILABILITY AND IMPLEMENTATIONWeb Browser: http://geval.sanger.ac.uk, Plugin: http://wchow.github.io/wtsi-geval-pluginCONTACTkj2@sanger.ac.ukSUPPLEMENTARY INFORMATIONSupplementary data are available at Bioinformatics online. |
| Author | Chow, William Brugger, Kim Torrance, James Caccamo, Mario Sealy, Ian Howe, Kerstin |
| Author_xml | – sequence: 1 givenname: William surname: Chow fullname: Chow, William organization: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK – sequence: 2 givenname: Kim surname: Brugger fullname: Brugger, Kim organization: East Anglian Medical Genetics Centre, Cambridge University Hospitals, NHS Foundation Trust, Cambridge CB2 0QQ, UK – sequence: 3 givenname: Mario surname: Caccamo fullname: Caccamo, Mario organization: National Institute of Agricultural Botany, Cambridge CB3 0LE, UK – sequence: 4 givenname: Ian surname: Sealy fullname: Sealy, Ian organization: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK – sequence: 5 givenname: James surname: Torrance fullname: Torrance, James organization: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK – sequence: 6 givenname: Kerstin surname: Howe fullname: Howe, Kerstin organization: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/27153597$$D View this record in MEDLINE/PubMed |
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