Next-generation sequencing (NGS) is now a commonplace tool for molecular characterisation of virtually any species of interest. Despite the ever-increasing use of NGS in laboratories worldwide, there are currently no freely available, integrated, simple-to-use, and standardised tools for analysing large volumes of raw NGS data from start to finish. We describe a haploid (bacterial and viral) NGS pipeline, SPANDx, which integrates multiple freely available software packages for NGS data analysis into a single tool. SPANDx can process large volumes of NGS data from the Illumina, Ion PGM and 454 platforms and requires minimal hands-on time. Using raw NGS data as input, SPANDx generates multiple user-friendly variant analysis outputs. SPANDx uses BWA for alignment of raw NGS reads against a reference genome or pan-genome, followed by variant calling and annotation using Picard, the GATK, SAMTools and SnpEff, and locus presence/absence determination using BEDTools to define the core and accessory genomes. High-confidence core single-nucleotide matrices (VCFtools and the GATK) generated by SPANDx can be directly imported into PAUP*, PHYLIP or RAxML for downstream phylogenetic analysis. SPANDx has been developed to handle NGS data from Illumina, Ion Personal Genome Machine (PGM) and 454 platforms, and we demonstrate that it has comparable performance across Illumina MiSeq/HiSeq2000 and Ion PGM data. SPANDx is a simple-to-use, high-throughput, open source and integrated tool that uses well-validated programs for comprehensive haploid NGS analysis. SPANDx has specifically been designed to perform robust analysis of raw haploid NGS datasets from beginning to end and is capable of task parallelisation, resulting in rapid turn-around-time. It is anticipated that SPANDx will be used as a standardised tool for comparing haploid NGS data outputs across research groups, thereby streamlining and simplifying bioinformatic analyses.