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

Dear Nestor,

I have used them only with Illumina data but I don't recall that they cannot
be used with 454 paired reads. Is it explicitly mentioned anywhere?

In case you are using Velvet, SOPRA can be run in integration with Velvet
and the authors suggest that is better than running SOPRA separately
post-assembly although I have not tried using it this way (yet). Good luck!

-Surya

On Fri, Jul 15, 2011 at 12:21 PM, Nestor Zaburannyi <nestor@xxxxxxxxxxxxx>wrote:

> Dear Surya,
>
> > 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
>
> Thanks, already gave SSPACE a try. It is good, pity only for short reads as
> i understand. Will also try also SOPRA.
>
>
> > 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
>
>
> >> --
> >> You have received this mail because you are subscribed to the mira_talk
> >> mailing list. For information on how to subscribe or unsubscribe, please
> >> visit http://www.chevreux.org/mira_mailinglists.html
>
>
>
>
> --
> З повагою,
>  Nestor                            mailto:nestor@xxxxxxxxxxxxx
>
>
> --
> You have received this mail because you are subscribed to the mira_talk
> mailing list. For information on how to subscribe or unsubscribe, please
> visit http://www.chevreux.org/mira_mailinglists.html
>

Other related posts: