SPANDx protocols

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description
SPANDx computational protocol

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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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 IN pipelines

 (2)
2017
PMCID: 5681832
PMID: 29126393
DOI: 10.1186/s12864-017-4216-2

[…] 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]. […]

2015
PMCID: 4551764
PMID: 26311542
DOI: 10.1186/s12864-015-1857-x

[…] influenzae. instead, we aimed to identify discrete, h. influenzae-specific genetic loci for assay design. to identify such loci, the coveragebed module of bedtools v2.18.2 [34], which is part of the spandx pipeline, was applied across the 246 closely related haemophilus genomes as described previously [35], using default settings. this tool performs presence/absence analysis of illumina reads […]

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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