Alignment: where does the read go on the ref

genomereaadgenome

------rea-d------

based on: does the base match; then how many errors allowed; scores for mismatch etc

Mapping: does the read match the ref

does “read” map to “genomereaadgenome”? yes/no

based on some score

Ref

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.”