[mira_talk] Re: Where are my scaffolds?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 17 Aug 2009 00:09:56 +0200
On Freitag 14 August 2009 Marcin Swiatek wrote:
> I seem to have difficulties getting good results from Mira. Or perhaps
> 'expected' would be a better word. Here is my story: I am trying to
> assemble the genome of a strain of a Lactobacillus bacteria. It is a
> naughty little microbe [...]
Hi Marcin,
welcome to the club. Lactobacillus has been a nightmare project also for me.
Especially as I had no paired-end at the time.
> I got decently looking results, but there is one thing I
> don't understand: where all these paired ends went? They are in the input
> files I think, I saw these reads in the generated traceinfo file...
My first guess would be: in the contigs, where they belong.
> However, while both Celera and Newbler produced contigs *and* scaffolds, in
> Mira's output I find contigs only.
In the beginning the users I know liked to use MIRA and combine it with
dedicated scaffolders (BAMBUS, own scripts etc.), therefore I never really
felt the urge to implement an own scaffolder. This has considerably changed as
inquiries for a scaffolder have noticeably increased in the past year. I think
I'll have to cave in at some point: not for the 3.0 version which I'm
finalising at the moment, but it's now pretty high on the TODO.
In the mean time, some time ago I had asked a few people who I know use the
AMOS scaffolder to write a short HOWTO for data comming from MIRA. But I
haven't heard back from any at the moment.
> Contigs computed by Mira (using
> 'accurate') are quite similar in number and size distribution to what I get
> with other assemblers, but I see no scaffolds and no evidence of use of
> paired end data.
> [...]
> Now the questions. Firstly, how do I tell if paired ends were indeed used
> or not. Secondly, if they weren't, how do I go about putting them to use.
MIRA uses them without making too much noise about it. One way for you to
check: in the output, there's a line saying
Generated XXX unique template ids for YYY valid reads.
If XXX is smaler than YYY, then MIRA has assigned read-pairs to templates and
uses that information later on in the assembly:
[1321] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
[1381] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++s+
[1440] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
[1500] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
[1560] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
[1620] ++++++++++++++++++++++++++++++++++++++++++++++++++t+t+t+++++
The "+" shows reads assembled without problems, "s" means a read has been
rejected at a given contig position because of template size violation and "t"
because of template direction violation. So you'll see the template usage only
when there's a (temporary) problem during construction, all others are
assembled without any more notice.
> And if they were, why don't I see scaffolds (or longer contigs with little
> gaps in them).
Because there's no scaffolder. As I wrote, it's on the TODO. In the mean time,
I'd propose to use the one from AMOS as I heard it works quite well (never
used it though).
> I will have another query, but I think I will try that one by one.
No problem.
Best,
Bastien
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