NGS Genome Browser Survey

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Evaluation of Viewers

Category Package Vender Generalizability (Sensitivity in proposal) Accuracy (Specificity) Performance Compatibility Usability Latest update
Viewer
Viewer


Summary of Viewers

Package Description Performance experience NBIC user
LookSeq It is an interactive AJAX-based web viewer for browsing large data sets of aligned sequence reads. By enabling seamless browsing and fast zooming, the LookSeq program assists the user to assimilate information at different levels of resolution, from an overview of a genomic region to fine details such as heterogeneity within the sample. LookSeq provides a simple graphical representation of paired sequence reads that is more revealing about potential insertions and deletions than are conventional methods. pubmed None
EagleView genome viewer EagleView is an information-rich genome assembler viewer with data integration capability. EagleView can display a dozen different types of information including base qualities, machine specific trace signals, and genome feature annotations. None
XMatchView A visual tool for analyzing cross_match alignments. Developed by Rene Warren and Steven Jones at Canada's Michael Smith Genome Sciences Centre. Python/Win or Linux. None
MapView Visualization of short reads alignment on desktop computer. None
HawkEye An Interactive Visual Analytics Tool for Genome Assemblies. None
Haplowser Haplowser: comparative haplotype browser for personal genome and metagenome pubmed. None
UTGB toolkit The UTGB (University of Tokyo Genome Browser) Toolkit is designed to meet three major requirements for personalization of genome browsers: easy installation of the system with minimum efforts, browsing locally stored data and rapid interactive design of web interfaces tailored to individual needs. The UTGB Toolkit is licensed under an open source license. The software is freely available at http://utgenome.org/. pubmed None

Available Sequence Viewers*

Package Web-based Standalone
ABySS-Explorer x
MapView x
CLC Genomics Workbench x
MaqView x
Consed x
Orchid x
DNASTAR Lasergene x
Sequencher x
EagleView x
SAMtools x
tview x
Gap x
Integrative Genomics Viewer (IGV) x
LookSeq x
Hawkeye x
NCBI Assembly Archive Viewer x

Available Genome browsers*

Package Web-based Standalone
Argo x
CGView x
Gaggle x
Integrative Genomics Viewer (IGV) x
Integrated Genome Browser (IGB) x
NCBI Genome Workbench x
Ensembl x
Genome Projector x
JBrowse x
JGI x
NCBI Map Viewer x
UCSC Genome Browser x
UCSC Cancer Genomics Browser x
X:map x
Cancer Molecular Analysis Portal x
AnnoJ x
Gbrowse x

On data interoperability

Interoperability Task Force is working on a system that manages biological data heterogeneity and provides interoperability using open and extensible standards and methodologies. The development of genomic visualization software could be benefited from these open and standard data access technology.

  • The data exchange format and APIs should be agreed upon. We can select from a set of stardard ones.
  • Interoperability Task Force could provide standard APIs for enriching the displayed information in genome browsers.
  • The annotations created by researchers in visualization software should be inserted into a suitable knowledge store seamlessly.