Hash Table Background

The DRAGEN mapper extracts many overlapping seeds (subsequences or K-mers) from each read, and looks up those seeds in a hash table residing in memory on its PCIe card, to identify locations in the reference genome where the seeds match. Hash tables are ideal for extremely fast lookups of exact matches. The DRAGEN hash table must be constructed from a chosen reference genome using the dragen --build-hash-table option, which extracts many overlapping seeds from the reference genome, populates them into records in the hash table, and saves the hash table as a binary file.