There is a new GBrowse paper by Lincoln Stein out in Briefings in Bioinformatics, entitled Using GBrowse 2.0 to visualize and share next-generation sequence data, PMID:23376193 [1]
Abstract:
GBrowse is a mature web-based genome browser that is suitable for deployment on both public and private web sites. It supports most of genome browser features, including qualitative and quantitative (wiggle) tracks, track uploading, track sharing, interactive track configuration, semantic zooming and limited smooth track panning. As of version 2.0, GBrowse supports next-generation sequencing (NGS) data by providing for the direct display of SAM and BAM sequence alignment files. SAM/BAM tracks provide semantic zooming and support both local and remote data sources. This article provides step-by-step instructions for configuring GBrowse to display NGS data.
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named PMID:23376193