Next generation sequencing can produce anywhere from hundreds of thousands to tens of millions short nucleotide sequences for a single sample.  For any given base within an individual sequence there can also be a quality score associated with the confidence of that base call from the sequencer.  The process of alignment is used to map all of these reads to a reference sequence, providing information with regards to the start and stop positions of each read within the reference sequence as well as a quality metric for the mapping.  These aligned reads can then be utilized for downstream tasks such as variant detection or expression analysis.  This document will provide information about the available aligners within Partek® Flow® as well as illustrate how to perform alignment against a reference sequence.

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