Question: Need library for implementation of DNA Alignment
1
gravatar for plabanbiswas96
9 weeks 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 • 251 views
ADD COMMENTlink modified 9 weeks ago by Brian Bushnell13k • written 9 weeks ago by plabanbiswas9610
1
gravatar for Pierre Lindenbaum
9 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum96k wrote:

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

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by Pierre Lindenbaum96k

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

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by plabanbiswas9610

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

ADD REPLYlink written 9 weeks ago by Pierre Lindenbaum96k

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 9 weeks ago • written 9 weeks ago by plabanbiswas9610
0
gravatar for Brian Bushnell
9 weeks ago by
Walnut Creek, USA
Brian Bushnell13k wrote:

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

ADD COMMENTlink written 9 weeks ago by Brian Bushnell13k

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 8 weeks ago by plabanbiswas9610
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