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genomereaadgenome
------rea-d------
based on: does the base match; then how many errors allowed; scores for mismatch etc
does “read” map to “genomereaadgenome”? yes/no
based on some score
from the ARKS paper
https://doi.org/10.1186/s12859-018-2243-x
“First, for the sake of argument, we make a clear distinction between the terms “alignment” and “mapping”: while the former refers to inferring the relative coordinates of bases between a query and a target, the latter is about determining if the query sequence hits a particular target.”