Physical mapping Read mapping Short read alignment Oligonucleotide mapping Oligonucleotide alignment Read alignment 1.1 The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences. Align short oligonucleotide sequences (reads) to a larger (genomic) sequence. Short oligonucleotide alignment Short read mapping Oligonucleotide alignment construction Short sequence read mapping Oligonucleotide alignment generation Sequence read processing