Abstract
We developed a program JVM (Java Visual Mapping) for mapping next generation sequencing read to reference sequence. The program is implemented in Java and is designed to deal with millions of short read generated by sequence alignment using the Illumina sequencing technology. It employs seed index strategy and octal encoding operations for sequence alignments. JVM is useful for DNA-Seq, RNA-Seq when dealing with single-end resequencing. JVM is a desktop application, which supports reads capacity from 1 MB to 10 GB.
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© 2015 Shanghai Jiaotong University Press, Shanghai and Springer Science+Business Media Dordrecht
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Yang, Y., Liu, J. (2015). JVM: Java Visual Mapping Tool for Next Generation Sequencing Read. In: Wei, D., Xu, Q., Zhao, T., Dai, H. (eds) Advance in Structural Bioinformatics. Advances in Experimental Medicine and Biology, vol 827. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9245-5_2
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DOI: https://doi.org/10.1007/978-94-017-9245-5_2
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