[mira_talk] Re: Assembly finishing
- From: Sven Klages <sir.svencelot@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 15 Apr 2009 11:01:42 +0200
Hi Lionel,
2009/4/14 Lionel Guy <guy.lionel@xxxxxxxxx>
> Hi there,
>
> I have an issue that is somewhat weakly related to mira...
>
> I am currently using consed to finish assemblies (checking misassemblies,
> designing primers for PCR, adding PCR-product end-sequencing results,
> etc...). I'm only half-satisfied with that solution, for several reasons,
> and would like to explore new possibilities, and have a couple of questions:
>
What's wrong with consed?
The only real issue that is annoying me (as a consed user) is how consed
deals with consensus
generation. That is especially problematic with refguided assemblies using
Illumina/454 reads,
where there is the reference sequence always representing the consensus;
there's no new consensus
generation after removal of reference sequence ...
>
> - Is there a way to display the IUPc, UNSc, SRMc, WRMc, etc. tags in
> consed? I have tried, but not succeeded so far
> - Is there any alternative to consed (or to gap4, that is not really
> suitable if you have half a million reads)?
>
I still like gap4. The more tags you have the slower gets gap4 ... the gap5
is far from being stable, even the
assembly file format is subject to change. But I do agree with Bastien:
YippiYeah!
I have played around with commercial software like CLC Genomics WB and
Lasergene's DNAStar, but none
of them fits our needs of "finishing a sequencing project".
So am eagerly waiting for gap5 too...
Tools like hawkeye and/or eagleview are somewhat helper applications for the
finishing process,
we are sporadically using hawkeye ...
hth,
Sven
> I would be very pleased if you would share your experience in that
> matter...
>
> Best,
>
> Lionel
>
>
> --
> You have received this mail because you are subscribed to the mira_talk
> mailing list. For information on how to subscribe or unsubscribe, please
> visit http://www.chevreux.org/mira_mailinglists.html
>
Other related posts:
