Hash table based mapping. The flow chart of hash table based mappers. 1) Divide the query read into smaller k-mers. 2) Search each k-mer in the hash table which is previously generated from the reference genome. 3) Probe location lists. 4) Retrieve the reference sequence starting at the seed location. 5) Align the read against the reference sequence. 6) Move to the next location and redo steps 4 and 5.
Xin et al. BMC Genomics 2013 14(Suppl 1):S13 doi:10.1186/1471-2164-14-S1-S13