[mira_talk] Re: Problem with Paired 454, MP Illumina, MIRA and Bambus

  • From: Surya Saha <ss2489@xxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 14 Jul 2011 15:10:54 -0400

Hi Nestor,

I have had moderate luck with two scaffolders besides the ones already
mentioned. You might want to try them out.

SSPACE (
http://www.baseclear.com/sequencing/data-analysis/bioinformatics-tools/sspace/
)
SOPRA (http://www.physics.rutgers.edu/~anirvans/SOPRA/)

-Surya

2011/7/12 Nestor Zaburannyi <nestor@xxxxxxxxxxxxx>

> Dear Bastien,
>
> Thanks for your hints. Indeed, dirty hack involving the reversal of both MP
> read sets helped.
>
> Regards
> Nestor
>
> > On Jul 6, 2011, at 23:19 , Nestor Zaburannyi wrote:
> >> I have 454 paired data and Illumina Mate-Pair data. It took me some time
> to figure out that not the Bambus is wrong... Long story short:
>
> > Actually I am not so sure that Bambus is correct :-)
>
> > One thing to keep in mind are the orientation of the pairs and what the
> scaffolder expects:
> > - Sanger pairs are oriented like this:   ------>    <--------  and that
> is what Bambus wants per default
> > - 454 pairs are originally oriented like this:  -------->    --------->
> but as scaffolders (and MIRA) originally did not expect that, I use a trick
> by letting sff_extract reverse one sequence so that everything as back to
> "normal". Nowadays MIRA could also use the forward / forward orientation,
> but I had not time to change sff_extract.
> > - Illumina paired-end reads look like this:    -------->   <---------
>  ... which makes it easy.
> > - Illumina mate-pairs look like this:    <---------    ---------->    ...
> which again lets scaffolders like Bambus despair as the expect something
> different. MIRA does not care there, it can work with that, too.
>
> >> Most of the contigs are not joined properly and we get hundreds of
> thousands "Invalid" links with consistent distance between them. Something
> like:
>
> > Which is a symptom of what I described: mate-pairs are facing outwards,
> Bambus expects them to face inwards.
>
> > There is no easy solution to this, the simplest one I can think of is to
> reverse all reads of the Illumina mate-pair set (both sets!) and then
> assemble. Should keep Bambus happy.
>
> > Hope that helps,
> >   Bastien
>
>
>
>
>
>
> --
> З повагою,
>  Nestor                            mailto:nestor@xxxxxxxxxxxxx
>
>
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