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Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.





To see what versions of minialign are available, and if there is more than one, which is the default, along with some help, type

module spider minialign

To see what other modules are needed, what commands are available and how to get additional help type

module help minialign

To use minialign, include a command like this in your batch script or interactive session to load the minialign module: (note ‘module load’ is case-sensitive):

module load minialign