SPANDx pipeline

SPANDx specifications

Information


Unique identifier OMICS_17827
Name SPANDx
Alternative name Synergised Pipeline for Analysis of NGS Data in Linux
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data P/A matrix and single-nucleotide polymorphism (SNP) matrices.
Output format nex
Operating system Unix/Linux
Programming languages Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Version 3.2
Stability Stable
Requirements Portable Batch System, Java, Genome Analysis Tool Kit
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Derek Sarovich <>

Additional information


GATK needs to be downloaded and installed separately due to Broad Institute licencing restrictions. Commercial users of GATK are required to obtain a licence for use. For further information, see www.appistry.com/ gatk. As of version 3.1, GATK is open source to not-for-profit institutions only. PLINK has not been included in the SPANDx bundle yet, but will be included in future versions.

Publication for Synergised Pipeline for Analysis of NGS Data in Linux

SPANDx citations

 (2)
2017
PMCID: 5681832

[…] setting except in adjusting segment length to 1000 bp resulting in a p. putida core genome of 2,068,252 bp and a p. aeruginosa core genome of 6,193,571 bp. core genome snps were called using spandx (version 3.1) [35]. a maximum-likelihood tree was then estimated using raxml (version 8.2.6) with a gtr substitution model and gamma distribution of rates undergoing 1000 bootstraps [36]. […]

2016
PMCID: 5359412

[…] brennan et al., 2013)., we aligned sequence data from existing isolates (stinear et al., 2014) and newly generated sequences against the jkd6159 reference genome (st93, genbank: cp002114), using spandx v2.6, with default parameters to produce a core alignment (sarovich & price, 2014). orthologous snps were used for phylogenetic reconstruction using raxml (stamatakis, 2014). mobile […]

SPANDx institution(s)
Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Casuarina, NT, Australia; Child Health Division, Menzies School of Health Research, Charles Darwin University, Casuarina, Darwin, NT, Australia
SPANDx funding source(s)
Supported by the Australian National Health and Medical Research Council via award 1046812.

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