Hash Table Background

The DRAGEN mapper extracts overlapping seeds (subsequences or K-mers) from each read. DRAGEN looks up the seeds in a hash table that resides in memory on the PCIe card to identify locations in the reference genome where the seeds match. Hash tables are ideal for 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.