GBrowse and Next Generation Sequencing Data

From the GBrowse mailing list comes word of some guidance for folks dealing with all that NGS data.  There’s a poster and a text tutorial on how to configure GBrowse to display the data.

Hello all,

Two resources are now available explaining how to use GBrowse, the Bio::DB::Sam adaptor, and SAMtools to visualize next generation sequence (NGS) data in GBrowse:

GBrowse and Next Generation Sequencing Data

http://gmod.org/wiki/Image:GBrowse_nextgen_poster.pdf

This poster by Scott Cain (and others) explains how to use Bio::DB::Sam and SAMtools with GBrowse 1.70 and GBrowse 2.  Previously SAMtools could only be used with GBrowse 2.

GBrowse NGS Tutorial

http://gmod.org/wiki/GBrowse_NGS_Tutorial

This step by step tutorial walks you through configuring GBrowse 2 to display data in SAMtools databases.  It includes a VMware image to work with, and uses the example human data that is included with SAMtools.

Please let Scott or myself know if you have any questions.

Thanks,

Dave C.

GMOD Help Desk

Recently Galaxy has also added some NGS analysis tools to its collection as well (look down at the bottom left of the tools list).  They are in beta, but if you are swamped with this kind of data these might be of use.

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