Welcome to Japsa’s documentation!

Japsa is a free, open source JAva Package for Sequence Analysis. It contains a range of analysis tools that biologists and bioinformaticians would routinely use but may not be available elsewhere. It also provides a Java library to be incorporated in other Java projects.

The package aims to be lightweight (fast and memory efficient) and to use the least possible dependencies. Its tools have a consistent command line interface and support reading from/writing to streams whenever possible.

Japsa and its source code is licensed under the BSD license and is available on GitHub.

Contents:

• 1. Dependencies
• 2. Installation
  • 2.1. Install from the pre-compiled package
  • 2.2. Obtain source code and compile
• 3. Usage convention
  • 3.1. Naming
  • 3.2. General usage
• 4. List of tools
  • 4.1. jsa.seq.stats: Show statistics of sequences
  • 4.2. jsa.seq.sort: Sort the sequences in a file
  • 4.3. jsa.seq.extract: Extract subsequences from a genome
  • 4.4. jsa.seq.split: Split multiple sequence file
  • 4.5. jsa.seq.join: Join multiple sequences into one file
  • 4.6. jsa.seq.annovcf: Annotate a vcf file
  • 4.7. jsa.seq.gff2fasta: Extract gene sequences
  • 4.8. jsa.seq.emalign Align two sequences using EM
  • 4.9. jsa.hts.countReads: Count reads from bam files
  • 4.10. jsa.hts.errorAnalysis: Error analysis of sequencing data
  • 4.11. jsa.hts.n50: Compute N50 of an assembly
  • 4.12. npReader: real-time conversion and analysis of Nanopore sequencing data
  • 4.13. jsa.np.filter: Filter sequencing data
  • 4.14. jsa.np.rtSpeciesTyping: Bacterial species typing with Oxford Nanopore sequencing
  • 4.15. jsa.np.rtMLST: Multi-locus Sequencing Typing in real-time with Nanopore sequencing
  • 4.16. jsa.np.rtStrainTyping: Bacterial strain typing with Oxford Nanopore sequencing
  • 4.17. jsa.np.rtResistGenes: Antibiotic resistance gene identification in real-time with Nanopore sequencing
  • 4.18. npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
  • 4.19. barcode: real-time de-multiplexing Nanopore reads from barcode sequencing
  • 4.20. jsa.util.streamServer: Receiving streaming data over a network
  • 4.21. jsa.util.streamClient: Streams data over a network
  • 4.22. XMas: Robust estimation of genetic distances with information theory
  • 4.23. jsa.phylo.normalise: Normalise branch length of a phylogeny
  • 4.24. capsim: Simulating the Dynamics of Targeted Capture Sequencing with CapSim
  • 4.25. Expert Model: tool for compression of genomic sequences
• 5. Credits
• 6. License

Indices and tables

• Index
• Module Index
• Search Page