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

  • From: Evan <evan@xxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 21 Jul 2011 09:21:47 -0700

Once I have contigs that have been scaffolded with one of the tools
mentioned (Thanks everyone for brining these to my attention), what are the
best Mira parameters to help fill in some of the gaps of NNNNN's?

Thanks

On Sun, Jul 17, 2011 at 3:55 AM, WATSON Mick <mick.watson@xxxxxxxxxxxxxxx>wrote:

> I'd be interested in this rewrite if you want to share it? I'd like to see
> Novoalign implemented too :)
>
> Sent from Samsung Mobile
>
>
> Robin Kramer <kodream@xxxxxxxxx> wrote:
>
>
> We rewrote SSPACE to use bwa.
>
> On Fri, Jul 15, 2011 at 10:46 AM, Nestor Zaburannyi <nestor@xxxxxxxxxxxxx
> <mailto: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<mailto: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/<
> http://www.physics.rutgers.edu/%7Eanirvans/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<mailto:
> 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
> <mailto:nestor@xxxxxxxxxxxxx>
>
>
> >> >> --
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>
> >> --
> >> З повагою,
> >>  Nestor                            mailto:nestor@xxxxxxxxxxxxx<mailto:
> nestor@xxxxxxxxxxxxx>
>
>
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>
>
> --
> З повагою,
>  Nestor                            mailto:nestor@xxxxxxxxxxxxx<mailto:
> nestor@xxxxxxxxxxxxx>
>
>
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