[mira_talk] Re: Assembly finishing

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
>
>
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