Question: Open Source Java De Novo Assembly Software
1
gravatar for lyz10302012
6.2 years ago by
lyz10302012330
China
lyz10302012330 wrote:

Is there any open source java de novo assembly softwares or de bruijn graph algorithms?

Thanks

ADD COMMENTlink modified 6.1 years ago by Chris Whelan540 • written 6.2 years ago by lyz10302012330
1

Do you mean stuff that actually works on real data, or just for information/investigation?

ADD REPLYlink written 6.2 years ago by zam.iqbal.genome1.7k

I mean stuff that actually works on real data.

ADD REPLYlink written 6.1 years ago by lyz10302012330
2

Ah. Well in that case I have never heard of one I'm afraid. Genome assembly is quite memory hungry, and so I think people tend to want to maintain very tight control of how they allocate and release memory. I could be wrong, there have been a lot of assemblers written, and you might find one that works on bacterial data - but if so I expect someone will reply here to tell us. best Zam

ADD REPLYlink written 6.1 years ago by zam.iqbal.genome1.7k

I agree. De novo assembly is the most memory demanding application in computational biology, while Java is notorious for its huge memory consumption. We can hardly see how they fit together...

ADD REPLYlink written 6.1 years ago by lh331k
1
gravatar for Rayan Chikhi
6.1 years ago by
Rayan Chikhi1.4k
France, Lille, CNRS
Rayan Chikhi1.4k wrote:

There exists one open-source Java software that constructs the de Bruijn graph (but it does not assemble). http://grafia.cs.ucsb.edu/msp/download.html

There does not appear to exist any open source de novo assembler written in Java.

Source: http://seqanswers.com/wiki/Special:BrowseData/Bioinformatics_application?Language=Java&Bioinformatics_method=Assembly&Biological_domain=De-novo_assembly

EDIT:

Indeed, Contrail can be considered as a de novo assembler written in Java.

ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by Rayan Chikhi1.4k
0
gravatar for Chris Whelan
6.1 years ago by
Chris Whelan540
Portland, OR
Chris Whelan540 wrote:

This is probably not exactly what you are looking for, but Michael Shatz's group is working on a Hadoop-based de Bruijn graph assembler called Contrail:

http://sourceforge.net/apps/mediawiki/contrail-bio/index.php?title=Contrail

Since it is a native Hadoop application it is mostly written in Java, although it appears that they also invoke other non-Java programs (FLASH and QUAKE) as part of their workflow.

This gets around the memory management features of Java that make a traditional single-machine algorithm hard to implement by using Hadoop's mechanisms of streaming data to and from disks across a cluster.

I am not sure what its state of readiness/current ability to run on real data is.

ADD COMMENTlink written 6.1 years ago by Chris Whelan540
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