Re: [AMOS-help] Bambus and scaffolding in general?

[Michael S. <ms...@um...>]

Hi Dan,

I strongly recommend you consider using a different assembler rather than
trying to scaffold the phrap assembly. Bambus does a very good job
scaffolding, but it is only as good as the contigs that it runs on. I
recommend you try either the Celera Assembler:
http://wgs-assembler.sourceforge.net or Arachne:
http://www.broad.mit.edu/wga/. Unlike phrap, both of these assembler make
use of mate-pairs directly, and both assemblers recognize and assemble
repeats better than phrap. AMOS has full support for the Celera Assembler,
if for example, you want to view the assembly results in Hawkeye.

Here is the manual for the current release of Celera Assembler:
http://apps.sourceforge.net/mediawiki/wgs-assembler/index.php?title=Version_5.2_runCA_Documentation

Good luck!

Mike Schatz



On Wed, Nov 5, 2008 at 11:39 AM, Dan Bolser <dan...@gm...> wrote:

> Hi all,
>
> I was about to start looking at Bambus for scaffolding some Sanger
> reads assembled by phred/phrap... However, before I start I would like
> to ask:
>
> Is Bambus the best / most commonly used scaffolding program?
>
> Which other programs should I be also looking at?
>
> Can I combine BAC end sequence links (obtained by blast) along with
> mate-pair links? (I should just read the manual for this one I know).
>
> Thanks very much for help,
>
> Dan.
>
>
> --
> http://network.nature.com/profile/dan
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