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 alphatical order) have contributed to the development of Japsa, including ideas, algorithms, implementation, documentation and feedback:
- Bhuvan Sankar
- David Powell
- Devika Ganesamoorthy
- Hoang Anh Nguyen
- Julia Bernal
- Lachlan Coin
- Lloyd Allison
- Michael Hall
- Mikael Boden
- 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.