[mira_talk] Re: Scaffolding contigs
- From: David Coil <coil.david@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 7 Oct 2013 09:22:44 -0700
I second the motion for having this discussion here as long as Bastien
doesn't mind. I think a lot of MIRA users are using SSPACE.
David
On Mon, Oct 7, 2013 at 8:57 AM, Adrian Pelin <apelin20@xxxxxxxxx> wrote:
> It doesn't need to go here, but I think is still very relevant, since we
> would be talking about scaffolding a mira assembly.
>
> I have not yet found how to get sspace to work nicely. I tried forcing it
> to scaffold multiple times using the same assembly, but not sure how
> reliable those results are.
>
> Sincerely,
> Adrian
>
> On Oct 7, 2013, at 11:39 AM, Shaun Tyler <Shaun.Tyler@xxxxxxxxxxxxxxx>
> wrote:
>
> I have some questions about optimising parameter settings for SSPACE that
> probably don't need to go to this group. If you don't mind discussing drop
> me a line at shaun.tyler@xxxxxxxxxxxxxxx.
>
>
>
> Shaun
>
>
> <graycol.gif>Jason Steen ---2013-10-01 10:53:56 PM---Sspace is good. The
> free version does a nice job using nextera matepair data that we have
> generated
>
>
> From: Jason Steen <j.steen2@xxxxxxxxx>
> To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
> Date: 2013-10-01 10:53 PM
> Subject: [mira_talk] Re: Scaffolding contigs
> Sent by: mira_talk-bounce@xxxxxxxxxxxxx
> ------------------------------
>
>
>
> Sspace is good. The free version does a nice job using nextera matepair
> data that we have generated.
>
>
> ---
>
> Dr Jason Steen
> Research Officer
> Australian Centre for Ecogenomics
> Ph : +61 7 3365 4957
> *www.ecogenomics.org* <http://www.ecogenomics.org>
>
>
>
> *From: *<Walter>, Mathias <*mathias@xxxxxxxxx* <mathias@xxxxxxxxx>>*
> Reply-To: *"*mira_talk@xxxxxxxxxxxxx* <mira_talk@xxxxxxxxxxxxx>" <*
> mira_talk@xxxxxxxxxxxxx* <mira_talk@xxxxxxxxxxxxx>>*
> Date: *Wednesday, 2 October 2013 4:58 AM*
> To: *"*mira_talk@xxxxxxxxxxxxx* <mira_talk@xxxxxxxxxxxxx>" <*
> mira_talk@xxxxxxxxxxxxx* <mira_talk@xxxxxxxxxxxxx>>*
> Subject: *[mira_talk] Re: Scaffolding contigs
>
> You can also try Opera and the scaffolder of SOAPdenovo.
>
> --
> Kind regards,
> Mathias
>
> 2013/10/1 Bastien Chevreux <*bach@xxxxxxxxxxxx* <bach@xxxxxxxxxxxx>>:
>
> On Oct 1, 2013, at 19:30 , Shaun Tyler
> <*Shaun.Tyler@xxxxxxxxxxxxxxx*<Shaun.Tyler@xxxxxxxxxxxxxxx>>
> wrote:
> We started playing with the newish Nextera mate-pair libraries and
> I'm wondering what people are doing for scaffolding MIRA assemblies.
> Right
> now I'm starting to look at SSpace and Bambus2 (Amos). Any comments,
> suggestions, advice ??
>
> Feedback from people here and off-list suggests SSpace to be a good
> first choice as it seems to be a lot easier to handle and get data into it
> than into Bambus.
>
> B.
>
>
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