4. List of tools

This chapter presents the list of tools provided by Japsa.

We are in the process of documenting 40+ tools, so stay tuned.

• 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