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 <[email protected]> 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 > > > > > ----- > > Confidentiality Notice: This e-mail and any files transmitted with it are > private and confidential and are solely for the use of the addressee. It may > contain material which is legally privileged. If you are not the addressee or > the person responsible for delivering to the addressee, please notify that > you have received this e-mail in error and that any use of it is strictly > prohibited. It would be helpful if you could notify the author by replying to > it. > > > > 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 >> <[email protected]> wrote: >> Hi, >> >> I would like to assemble 2 overlapping DNA sequences. Is there something in >> biojava that may help in this task? >> >> Thanks >> >> >> >> >> ----- >> >> Confidentiality Notice: This e-mail and any files transmitted with it are >> private and confidential and are solely for the use of the addressee. It may >> contain material which is legally privileged. If you are not the addressee >> or the person responsible for delivering to the addressee, please notify >> that you have received this e-mail in error and that any use of it is >> strictly prohibited. It would be helpful if you could notify the author by >> replying to it. >> >> >> >> >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
