Need library for implementation of DNA Alignment

Question

[plabanbiswas96]

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.

Answer 1

[Pierre Lindenbaum]

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

[plabanbiswas96]

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

[Pierre Lindenbaum]

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

[plabanbiswas96]

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.

[Pierre Lindenbaum]

https://blog.jayway.com/2013/06/10/how-to-use-make-and-makefile-in-maven-pom-xml/

Answer 2

[Brian Bushnell]

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

[plabanbiswas96]

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.