title: gEVAL - a web-based browser for evaluating genome assemblies.
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.
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: William
authors.initials: W
authors.lastname: Chow
authors.affiliation: East Anglian Medical Genetics Centre, Cambridge University Hospitals, NHS Foundation Trust, Cambridge CB2 0QQ, UK.
authors.forename: Kim
authors.initials: K
authors.lastname: Brugger
authors.affiliation: National Institute of Agricultural Botany, Cambridge CB3 0LE, UK.
authors.forename: Mario
authors.initials: M
authors.lastname: Caccamo
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Ian
authors.initials: I
authors.lastname: Sealy
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: James
authors.initials: J
authors.lastname: Torrance
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Kerstin
authors.initials: K
authors.lastname: Howe
mesh_terms: D000818:Animals; D016678:Genome; D023281:Genomics; D006801:Humans; D020407:Internet; D051379:Mice; D016415:Sequence Alignment; D064878:Web Browser