#8 Perfect k-mer hashing in Sailfish

The original version of Sailfish,
an RNA-Seq quantification tool, used minimal perfect hash functions to
replace k-mers with unique integers.
(The current version appears to be using a Cuckoo hashmap instead.)

This is my attempt to explain how a minimal perfect hash function could be
built. The algorithm described here is not exactly the same as the one
Sailfish used, but it follows the same idea.




Sections:


Sailfish and perfect hashing (1:15)
Perfect hashing based on binary search or hash tables (4:34)
Random hash functions (7:34)
Perfect hash function based on an acyclic graph (12:16)


Links:


The Sailfish paper
The paper describing the perfect hashing algorithm
The birthday paradox
Integrative Biology & Medicine





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