Welcome to Japsa

Japsa is a Java Package for Sequence Analysis. As the name implies, Japsa was written primarily in Java. It contains a large number of ready to run programs as well as a Java API.

Installation and Usage

Quick installation guide:

git clone https://github.com/mdcao/japsa
cd japsa
make install \
  [INSTALL_DIR=~/.usr/local \] 
  [MXMEM=7000m \] 
  [SERVER=true \] 
  [JLP=/usr/lib/jni:/usr/lib/R/site-library/rJava/jri]

Details of installation (including for Windows) and usage of Japsa can be found in its documentation hosted on ReadTheDocs

Authors and Contributors

Japsa was maintained by Minh Duc Cao (@mdcao). The following people (in no particular order) have contributed to the development of Japsa, including ideas, algorithms, implementation, documentation and feedback:

• Lachlan Coin
• Devika Ganesamoorthy
• Michael Hall
• Son Hoang Nguyen
• Mikael Boden
• Lloyd Allison
• Trevor I Dix
• Hoang Anh Nguyen
• Julia Bernal
• David Powell

Other projects based on Japsa

• eXpert Model: The expert model compression model
• XMas: Phylogenetic distance method using information theory
• capsim: Simulation of capture sequencing
• npScarf: Scaffold and Complete assemblies in real-time fashion
• npAnalysis: Realtime identification of bacterial sample
• npReader: Real-time extraction and analysis Oxford Nanopore sequencing data
• npBarcode: Demultiplex barcoded Oxford Nanopore sequencing
• PhageXpress

and more to come.

License

Japsa is released under the accompanying BSD-like license.