RT Journal Article
SR Electronic
T1 gEVAL – A web based browser for evaluating genome assemblies
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 038638
DO 10.1101/038638
A1 William Chow
A1 Kim Brugger
A1 Mario Caccamo
A1 Ian Sealy
A1 James Torrance
A1 Kerstin Howe
YR 2016
UL http://biorxiv.org/content/early/2016/02/02/038638.abstract
AB 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. While gEVAL focuses primarily on sequence integrity, it can also display arbitrary annotation including 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 Web Browser: http://geval.sanger.ac.uk, Plugin: http://wchow.github.io/wtsi-geval-plugin.Contact kj2{at}sanger.ac.ukSupplementary information Supplementary data are available at Bioinformatics online.