hsnguyen/japsa

Just Another JAva Package for Statistical Sequence Analysis

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. Please note that from our newest versions, it is required Java 8 to compile and run from the source code. Prebuilt releases would need JVM 1.8.0_144 or newer to run properly.

Installation and Usage

Quick installation guide:

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

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

Alternatively, build with maven (experimental). First you need to manually install JAR files that are not available on Maven public repo to your local repo. This can be achieved using the install_mvn.sh script provided.

./install_mvn.sh

mvn clean package install

you might need to try packaging Japsa again if failed. A SNAPSHOT is then created and you can invoke tool, e.g. species typer, by

java -cp ./target/japsa-1.0-SNAPSHOT.jar japsa.tools.bio.np.RealtimeSpeciesTypingCmd --bam <bam> --index <index>

Convenient scripts (like install by make) would be added soon.

Authors and Contributors

Japsa is currently maintained by Minh Duc Cao (@mdcao) and Son Hoang Nguyen. The following people (in alphatical order) have contributed to the development of Japsa, including ideas, algorithms, implementation, documentation and feedback:

• Allen Day
• Bhuvan Sankar
• David Powell
• Devika Ganesamoorthy
• Hoang Anh Nguyen
• Julia Bernal
• Lachlan Coin
• Lloyd Allison
• Michael Hall
• Mikael Boden
• Minh Duc Cao
• Son Hoang Nguyen
• Trevor I Dix

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 (abandoned)
• npAnalysis: Realtime identification of bacterial sample
• npReader: Real-time extraction and analysis Oxford Nanopore sequencing data
• npBarcode: Demultiplex barcoded Oxford Nanopore sequencing
• npGraph: Streaming scaffolding and visualisation (replacing npScarf)
• PhageXpress

and more to come.

License

Japsa is released under the accompanying BSD-like license.