High-performance sequence processing
6
Vectorized sequence parsing
PhD Thesis
Abstract
Introduction
1
Comparing genomic sequences
2
Comparing using k-mers
3
Sketching sequences
4
Sampling with minimizers
High-performance sequence processing
5
An intro to vectorization
6
Vectorized sequence parsing
7
Rolling hashes on sequences
8
Vectorized computation of minimizers
9
Application to sequence filtering
Locality-preserving representations of k-mer sets
10
Background on k-mer sets
11
Necklaces and minimizers
12
Set representation and operations
13
Super-k-mers maps
14
Sketching super-k-mers
Sampling k-mers to lower memory & complexity
15
Background on minimizers
16
Multiminimizers
17
Locally-consistent phrases
18
Lexicographic-informed sampling
Discussion & conclusion
References
High-performance sequence processing
6
Vectorized sequence parsing
6
Vectorized sequence parsing
See
helicase
, inspired by
(
Langdale & Lemire, 2019
)
Langdale
, G. &
Lemire
, D. (2019)
Parsing gigabytes of JSON per second
.
The VLDB Journal
,
28
, 941–960.
5
An intro to vectorization
7
Rolling hashes on sequences