primers-java

In progress Porting of Primer3 and PrimerPooler tools to java to be used as an API. Please note that:

Primer3 copyright are reserved to its authors (Andreas Untergasser, Ioana Cutcutache, Triinu Koressaar, Jian Ye, Brant C. Faircloth, Maido Remm and Steven G. Rozen)

PrimerPooler copyright are reserved to its authors (Silas S. Brown, Yun-Wen Chen, Ming Wang, Alexandra Clipson, Eguzkine Ochoa, and Ming-Qing Du)

Please if used in your work, cite:

For Primer3 : Untergasser A, Cutcutache I, Koressaar T, et al. Primer3--new capabilities and interfaces. Nucleic Acids Res. 2012;40(15):e115. doi:10.1093/nar/gks596

For PrimerPooler : Silas S. Brown, Yun-Wen Chen, Ming Wang, Alexandra Clipson, Eguzkine Ochoa, and Ming-Qing Du (2017). PrimerPooler: automated primer pooling to prepare library for targeted sequencing. Biology Methods and Protocols. Oxford University Press. 2(1). doi:10.1093/biomethods/bpx006

or both.

This is far from a clean API, use with caution.

Versions

The current version of the porting is :

• Primer3 : 2.4.0
• PrimerPooler : 1.5

TODO

• design a clean interface to use as API and add more documentation to the source code. Please note that the java version may contain undetected bugs and slower than the c version.
• Update and inlcude bugs fixes from lastest versions

Any comments, suggestion or issues are welcome.