gEVAL - a web-based browser for evaluating genome assemblies.
Bioinformatics
; 32(16): 2508-10, 2016 08 15.
Article
en En
| MEDLINE
| ID: mdl-27153597
ABSTRACT
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.
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Genómica
/
Navegador Web
Límite:
Animals
/
Humans
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2016
Tipo del documento:
Article
País de afiliación:
Reino Unido