The HeliSphere is an open-source LINUX software package intended for use in analyzing data produced by the HeliScope Single Molecule Sequencer. It consists of a set of core tools and analysis pipelines. The core tools are command line tools that perform unit functions such as alignment of reads to a reference, filtering of reads or alignments, report generation, file format conversions, etc. The pipelines organize sets of core tools to carry out a complex task, such as resequencing or digital gene expression analysis. The pipelines also provide managed parallel processing.

Note that in addition to the .html documentation, all tools take a --help argument which makes them print their parameter choices.