Japsa specifications

Information


Unique identifier OMICS_25250
Name Japsa
Alternative name JAva Package for Sequence Analysis
Software type Package/Module
Interface Command line interface, Application programming interface
Restrictions to use None
Biological technology Oxford Nanopore
Operating system Unix/Linux, Mac OS
Programming languages Java
License BSD-like license
Computer skills Advanced
Version 1.7-10a
Stability Stable
Requirements
JRE
Maintained Yes

Download


download.png

Versioning


No version available

Documentation


Maintainers


  • person_outline Lachlan Coin
  • person_outline Son Hoang Nguyen

Additional information


http://japsa.readthedocs.io/en/latest/index.html

Publication for JAva Package for Sequence Analysis

Japsa citation

library_books

Scaffolding and completing genome assemblies in real time with nanopore sequencing

2017
Nat Commun
PMCID: 5321748
PMID: 28218240
DOI: 10.1038/ncomms14515

[…] sFinder database. Plasmid origin of replication sequences in both K. pneumoniae assemblies were identified by uploading the assembly to the PlasmidFinder database.In real-time analysis, npScarf (from japsa version 1.6-06b) aligned incoming long reads using BWA-MEM with the parameters -k11-W20-r10-A1-B1-O1-E1-L0-a-Y-K10000. The -K10000 parameter allowed alignments to be streamed to the scaffolding […]

Japsa institution(s)
Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia; Department of Genomics of Common Disease, Imperial College London, London, UK

Japsa reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Japsa