Question: Need library for implementation of DNA Alignment
1
gravatar for plabanbiswas96
4 months ago by
plabanbiswas9610 wrote:

I am new to Bioinformatics. Can someone suggest a good library for DNA Alignment Library like BWA (not in Java) which can be used in Java and if possible output a SAM file.

sequencing alignment java • 287 views
ADD COMMENTlink modified 4 months ago by Brian Bushnell14k • written 4 months ago by plabanbiswas9610
1
gravatar for Pierre Lindenbaum
4 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum99k wrote:

I've written a java binding (JNI) for bwa: https://github.com/lindenb/jbwa

ADD COMMENTlink modified 4 months ago • written 4 months ago by Pierre Lindenbaum99k

When I compile through Maven, I get error stating cannot find symbol BWAServiceImplService.

ADD REPLYlink modified 4 months ago • written 4 months ago by plabanbiswas9610

where did you find that there is a maven-thing ? https://github.com/lindenb/jbwa#compilation

ADD REPLYlink written 4 months ago by Pierre Lindenbaum99k

Sorry for that but I required maven for building my college project (jbwa would be a great boost for it ) and also IntelliJ is not able to resolve this.bwaService=new BWAServiceImplService().getBWAServiceImplPort(); . Sorry for this but I am trying JNI for the first time and I am getting confused.

ADD REPLYlink modified 4 months ago • written 4 months ago by plabanbiswas9610
0
gravatar for Brian Bushnell
4 months ago by
Walnut Creek, USA
Brian Bushnell14k wrote:

BBMap is written in Java and can easily be called from Java.

ADD COMMENTlink written 4 months ago by Brian Bushnell14k

I have looked into BBMap. Is there a documentation of the java files (like purpose of each file) ? Also an example of mapping would be greatly appreciated.

ADD REPLYlink written 3 months ago by plabanbiswas9610
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