GenomeView

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3258165/figure/gkr995-F5/

Methods

linear single view single scale single focus segregated no abstraction no arrangement no interconnection segment sparse type segment contiguous type point sparse type point contiguous type

Tool

Access Format: web application Access Format: standalone app Supported Files: bed Supported Files: fasta Supported Files: sambamcram Supported Files: vcf Supported Files: other License: open source

Paper

GenomeView: a next-generation genome browser.

Abeel T, Van Parys T, Saeys Y, Galagan J, Van de Peer Y. GenomeView: a next-generation genome browser. Nucleic Acids Res. academic.oup.com; 2012;40: e12.

Cited by: 107

Abstract

Due to ongoing advances in sequencing technologies, billions of nucleotide sequences are now produced on a daily basis. A major challenge is to visualize these data for further downstream analysis. To this end, we present GenomeView, a stand-alone genome browser specifically designed to visualize and manipulate a multitude of genomics data. GenomeView enables users to dynamically browse high volumes of aligned short-read data, with dynamic navigation and semantic zooming, from the whole genome level to the single nucleotide. At the same time, the tool enables visualization of whole genome alignments of dozens of genomes relative to a reference sequence. GenomeView is unique in its capability to interactively handle huge data sets consisting of tens of aligned genomes, thousands of annotation features and millions of mapped short reads both as viewer and editor. GenomeView is freely available as an open source software package.