[mira_talk] Re: Fwd: ace file output from MIRA

Hi Bastien,

*** Bastien Chevreux (11.05.2009 23:05):
> On Sonntag 10 Mai 2009 Björn Nystedt wrote:
>> [...]
>> The basic problem is that MIRA does not create the .phd files.
> 
> Let me start my answer like Cato would have: "Ceterum censeo ACE esse 
> delendam."
> 
> There are no points for guessing correctly whether I like ACE or not ... it's 
> a horrible format for assemblies as it's missing half of the thing one needs 
> to fully encode an asembly.
> 

You are probably right, but many software packages use this format, for
output or for input ... and consed, to be honest, is not the worst
choice for genome assemblies :-)


> Well, that being said: MIRA reads PHD files, so I see no reason why it 
> shouldn't be able to write them :-)

Most people I know start from fasta/qual/xml. So they do not necessarily
have phd files ..


> 
> On the other hand: reading the consed docs for version 19.0, I see this 
> paragraph:
>   9.81)  Delete the phd.ball link in edit_dir--it is also intended for
>     obsolete versions of consed and may cause problems with the current
>     version.
> 
> Anyone who can comment on that?

In pre-19 versions consed was able to read phd.1 files from *one* huge
phd ball (cat'ed phed.1 files) for faster startup times.
In the current 19 versions all phd balls containing reads which were
used in the assembly are listed in the ace file.

That gives one the possibilty to use more than one phd ball,
which is definitely more efficient and flexible ..

> 
>> [...]
>> so maybe a wish would be for MIRA to output a full
>> consed folder similar to what Newbler does?
> 

That would be the best, as you have all the info/files you need
writing such structure ..

> If I only had a description of the format needed, that probably would be a 
> minor problem. I searched through the web to find one, but no luck. Or I am 
> blind, which is also a possibility.

I think the phred sources contain a format description; for short read
the phd header has been shortened ... I can send you a few examples when
I am back in Berlin (on wednesday) ..


Cheers,
Sven

> 
> Regards,
>   Bastien
> 
> 

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n:Klages;Sven
email;internet:sven.klages@xxxxxxxxxxxxxx
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