[mira_talk] Re: thanks!
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 6 Aug 2010 19:20:05 +0200
On Montag 02 August 2010 Davide Scaglione wrote:
> Again, your answers are always enlightening.
> I'm writing a chunk of my thesis on assembly algorithms...but most reviews
> don't cite so much MIRA, and I'm missing informations. If you know any
> review which cites thorougly MIRA, I will be glad if you send me a link.
Hmmm ... "reviews". I've seen some citing MIRA, but "thoroughly"?
Authoritative sources for MIRA are my PhD thesis, the article on miraEST in
Genome Research 2004 and the MIRA docs.
> On the meanwhile, could you please just tell me if MIRA belong to
>
> -OLC category (overlap/layout/consensus) or
> -deBrujin graph reduction or
> -greedy graph resolution.
> I wondered that it's more similar to OLC, cause the SKIM phase is only a
> "possible hits" sorting/screening, rather than a graph reduction...
MIRA does not really fit into any of these categories, certainly not into
deBruijn.
It has elements of both OLC and greedy though (the later was introduced with
454 where one really has to start to be a bit more selective), but these are
embedded into a learning framework which no other assembler I know of has.
If you really want to categorise MIRA, it could perhaps be described as
- iterative assembler learning from past mistakes with OLC and greedy
components
B.
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