PUBLICATION

gEVAL - a web-based browser for evaluating genome assemblies

Authors
Chow, W., Brugger, K., Caccamo, M., Sealy, I., Torrance, J., Howe, K.
ID
ZDB-PUB-160507-2
Date
2016
Source
Bioinformatics (Oxford, England)   32(16): 2508-10 (Journal)
Registered Authors
Caccamo, Mario, Howe (fka Jekosch), Kerstin
Keywords
none
MeSH Terms
  • Animals
  • Genome
  • Genomics*
  • Humans
  • Internet
  • Mice
  • Sequence Alignment
  • Web Browser*
PubMed
27153597 Full text @ Bioinformatics
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 CONTACT: kj2@sanger.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
Genes / Markers
Figures
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping