[Biojava-l] DNA assembly

[Chris Friedline]

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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