Comparative analysis of haploid next-generation genome sequence data

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SPANDx is your one-stop tool for identifying SNP and indel variants in haploid genomes using NGS data.

SPANDx performs alignment of raw NGS reads against your chosen reference genome or pan-genome, followed by accurate variant calling and annotation, and locus presence/absence determination. SPANDx produces SNP and indel matrices for downstream phylogenetic analyses. Annotated, genome-wide SNPs and indels can also be identified if specified, and are output in human readable format. A presence/absence matrix is also generated to allow you to identify the core/accessory genome content across all your genomes.

The outputs generated by SPANDx can be imported into PLINK for microbial genome-wide association study (mGWAS) analyses.

SPANDx can utilise PBS, SGE or SLURM for resource management. SPANDx can also run directly on the command line if no resource manager is available.

For the most up-to-date version of SPANDx, check us out on GitHub:

SPANDx Web Site


  • 30Nov16: SPANDx 3.2 now uses BWA-mem for faster more accurate alignments
  • 31May16: SPANDx 3.1.1 now works on pre-v2.3.1 TORQUE/PBS systems.
  • 14Feb16: SPANDx 3.1 The -z flag can now be set to include tri- and tetra allelic SNPs in the .nex outputs.
  • 26Dec15: SPANDx 3.0 has lots of upgrades including improved samtools compatibility, better PLINK integration for GWAS, and can call up to 9 indels and all four SNPs at a single locus!
  • 05Aug15: SPANDx v2.7 now works on SGE, PBS, SLURM, and systems without a resource manager.


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