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
- 3. Usage convention
- 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