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

  • From: Robin Kramer <kodream@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Fri, 15 Jul 2011 10:54:42 -0600

We rewrote SSPACE to use bwa.

On Fri, Jul 15, 2011 at 10:46 AM, Nestor Zaburannyi <nestor@xxxxxxxxxxxxx>wrote:

> Dear Surya,
>
> > 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 this topic there is mentioning of 454:
> http://seqanswers.com/forums/showthread.php?t=8350
>
> Apart from that, SSPACE is using bowtie with options that exclude any reads
> even with one mismatch. And this is hardly the truth for 454. Especially
> unclipped, raw data.
>
>
> > 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
>
>
> >> >> --
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>
>
>
>
> >> --
> >> З повагою,
> >>  Nestor                            mailto:nestor@xxxxxxxxxxxxx
>
>
> >> --
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>
>
>
> --
> З повагою,
>  Nestor                            mailto:nestor@xxxxxxxxxxxxx
>
>
> --
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