gEVAL-a web-based browser for evaluating genome assemblies

被引：27

作者：

Chow, William ^{[1
]}

Brugger, Kim ^{[2
]}

Caccamo, Mario ^{[3
]}

Sealy, Ian ^{[1
]}

Torrance, James ^{[1
]}

Howe, Kerstin ^{[1
]}

机构：

[1] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[2] NHS Fdn Trust, Cambridge Univ Hosp, East Anglian Med Genet Ctr, Cambridge CB2 0QQ, England

[3] Natl Inst Agr Bot, Cambridge CB3 0LE, England

来源：

BIOINFORMATICS | 2016年 / 32卷 / 16期

基金：

英国惠康基金;

关键词：

D O I：

10.1093/bioinformatics/btw159

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：2508 / 2510

页数：3

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