[mira_talk] Re: MIRA edits reads during assembly?

Hi Bastien,

On 25 Oct 2009, at 11:15 , Bastien Chevreux wrote:

let me start with an old citation: "Ceterum censeo, ACE esse delendam."

I do agree. But before there is another program to replace consed to finish assembly, or that consed developers change the format, I don't see any other issue than to find workarounds. Gap5 looks promising, but feature-wise, it's still far from reaching the level of consed...

By the way, have you heard about ABySS-Explorer? There was a paper in TVGC recently. Haven't seen the program at work yet, but it looks nice (http://www.computer.org/portal/web/csdl/doi/10.1109/TVCG.2009.116). Again, it's far from being a finishing program, but the graphical representation is quite interesting.

I hope that with "change" you mean: some are deleted. Other changes shouldn't
be.

Some bases are deleted in some reads, yes. Couldn't detect any other changes, indeed.

For 454 and Solexa reads, I wrote a much simpler editor which look for common overcall problems which it can safely delete. There's a whole set of rules behind it, but basically this editor wants a certain base to gap ratio, forward/reverse reads and a few things more before it decides to edit away a
base in a read.

OK, good to know...

Thanks for the answer! Parsing the reads from the caf files wasn't hard anyway. But for the sake of the poor souls that still use the damned ace format and consed, may I suggest that it might be interesting to have the possibility to output a phdball with convert_project?

Cheers,

Lionel
(Guy is actually my last name... know it's confusing given the email address)



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