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. This document will provide information about the available aligners within Partek ^® Flow ^® as well as illustrate how to perform alignment against a reference sequence.  The result of alignment will be an Aligned reads data node that contains the BAM files generated from the alignment.

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