[Biojava-l] DNA assembly

[Khalil El Mazouari]

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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>>> 
>>> 
>>> 
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