arnoldbaino/japsa

Just Another JAva Package for 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 a JAR file that is not available on Maven public repo to your local repo

mvn install:install-file \
 	-Dfile=./libs/colloquial.jar \
	-DgroupId=com.colloquial \
	-DartifactId=arithcode \
	-Dversion=1.1 \
	-Dpackaging=jar

then

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) 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
• 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.