the bioinformatics chat

#8 Perfect k-mer hashing in Sailfish

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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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      the bioinformatics chatBy Roman Cheplyaka
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