#8 Perfect k-mer hashing in Sailfish - a podcast by Roman Cheplyaka
from 2017-08-05T19:00
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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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Further episodes of the bioinformatics chat
Further podcasts by Roman Cheplyaka
Website of Roman Cheplyaka