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Gap5 1.2.0 release (assembly viewer & editor) jkbonfield Bioinformatics 78 10-03-2015 08:37 AM
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Old 04-06-2009, 04:24 AM   #1
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Default Gap5

I figured it's finally about time I actually released this, albeit still in a test variant and in dire need of documentation. However somewhat belatedly I'm concluding "release often, release early" paradigm of open source software is maybe correct.

NOTE: this is a test release and file formats *will* be changing during development. So be advised to keep copies of the old software if you want to upgrade to a new one as I cannot yet guarantee backwards compatibility. That's high up on the list of things to do though.

What is it? It's both an editor and a viewer for sequence assemblies, supporting both new short-read alignments as well as traditional capillary sequencers. Ie it's an upgrade to the trusty old Gap4 program. The editing side is where most of the more glaring bugs are (and you can't help but see some of them, so I consider it alpha quality for now), but it's also the most fun and challenging aspect. Data structures for efficient viewers are easy - tgap was doing that 2 years back with ease. However editing efficiently needs more thought.

The code has been in the Staden Package CVS tree for ages, but compiling is FAR from trivial as the build system needs a major overhaul. I put linux x86_64 and i686 binaries on sourceforge at:

Note that this is only a test release and I cannot really support it or provide different binaries if it doesn't work for you. I'm aware that there may be systems it fails on due to missing libraries or system incompatibilities. It was build in Debian Sarge (somewhat old), but should work on Etch. I haven't tested Debian Lenny or other linux vendors.

Documentation will come at some stage along with various screenshots, but for now I put up a copy of a recent internal talk on Gap5 at:

Sorry it's been so long in coming and despite that it not really being production quality yet either, but I may as well expose what I have to the masses. :-)

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