[Biojava-l] Genome Assembly

Wed Apr 24 18:24:44 UTC 2013

Hi !

I´m trying to assemble multiple reads using one as Reference, is this possile using Biojava ?

Greetings

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Enviados: Miércoles, 24 de Abril 2013 11:00:03
Asunto: Biojava-l Digest, Vol 123, Issue 10

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Today's Topics:

   1. Re: DNA assembly (Chris Friedline)

----------------------------------------------------------------------

Message: 1
Date: Wed, 24 Apr 2013 10:58:22 -0400
From: Chris Friedline <cfriedline at vcu.edu>
Subject: Re: [Biojava-l] DNA assembly
To: Andreas Prlic <andreas at sdsc.edu>
Cc: "Biojava-l at lists.open-bio.org" <biojava-l at lists.open-bio.org>,
	Khalil El Mazouari <khalil.elmazouari at gmail.com>
Message-ID: <DCB620AB-AE14-4A23-BCEE-BEB45D404BBA at vcu.edu>
Content-Type: text/plain;	charset=iso-8859-1

There's also a good deal of alignment quality checking, thresholding, and scoring the overlapping region that is both necessary and but maybe not all that straightforward.  I suggest that you check out the PANDAseq paper, which describes their algorithm.

http://dx.doi.org/10.1186/1471-2105-13-31

Andreas is correct - the basic building blocks are already there.

Chris

On Apr 24, 2013, at 10:48 AM, Andreas Prlic <andreas at sdsc.edu> wrote:

> It sounds like as all you need is to get the reverse complement of one of your sequences and then you do a local alignment. Both should be possible with BioJava...
> 
> Andreas
> 
> 
> On Wed, Apr 24, 2013 at 7:29 AM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
> Hi Chris,
> 
> my application is deployed as war file. I am trying to avoid, as much as possible, to shell out to other none java programs... for maintainability reasons.
> 
> I don't think I need a 'full' genome assembly tools (eg velvet ...), it's overkill for my case: cloned gene is sequenced on both directions. Normally one strand is sufficient. If the sequence quality is not good enough, the 2 strands are used to get the full length gene. There is always a large overlap between the 2 strand sequence.
> I can QC the full length gene.
> 
> Best
> 
> khalil
> 
> 
> 
> 
> 
> 
> 
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> 
> 
> 
> On 24 Apr 2013, at 16:04, Chris Friedline wrote:
> 
> > Khalil,
> >
> > Why not just shell out to programs designed for this purpose and pull in the results?  We are in the process of publishing a paper which uses PANDAseq to assemble overlapping PE reads.  The latest version of mothur also does this.
> >
> > www.mothur.org
> > https://github.com/neufeld/pandaseq/wiki/PANDAseq-Assembler
> >
> > PANDAseq is particularly nice in this case, because you could read right from stderr and stdout streams.  It's also wicked fast.
> >
> > Chris
> >
> > On Apr 24, 2013, at 4:08 AM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
> >
> >> Hi,
> >>
> >> It's not a global sequence alignment nor genome assembly. It's just a DNA fragment sequenced from both ends with an overlapping region. I want to assemble the 2 reads in order to get the full length sequence. This assembly is a part of a complex analysis process that uses biojava.
> >> I agree, there a lot of simple option how to achieve this. But I need somthing in java/biojava.
> >>
> >> Best
> >>
> >> khalil
> >>
> >>
> >>
> >>
> >> -----
> >>
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> >>
> >>
> >>
> >> On 23 Apr 2013, at 23:38, Spencer Bliven wrote:
> >>
> >>> If you just have two contiguous sequences to align, you should just use a global sequence alignment. See http://biojava.org/wiki/BioJava:CookBook3:PSA for how to do this in BioJava, or it might be easier to just use one of the online services for this such as http://www.ebi.ac.uk/Tools/psa/.
> >>>
> >>> On the other hand, if you actually want to do genome assembly (ie from many overlapping reads), then there are much more computationally efficient methods. BioJava isn't really intended for large-scale genome assembly, so you'd want to use a sequence assembly tool (eg Velvet).
> >>>
> >>> -Spencer
> >>>
> >>>
> >>> On Tue, Apr 23, 2013 at 12:38 PM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
> >>> Hi,
> >>>
> >>> I would like to assemble 2 overlapping DNA sequences. Is there something in biojava that may help in this task?
> >>>
> >>> Thanks
> >>>
> >>>
> >>>
> >>>
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