Succinct de Bruijn graphs
A Bowe, T Onodera, K Sadakane, T Shibuya - International workshop on …, 2012 - Springer
We propose a new succinct de Bruijn graph representation. If the de Bruijn graph of k-mers
in a DNA sequence of length N has m edges, it can be represented in 4 m+ o (m) bits. This is …
in a DNA sequence of length N has m edges, it can be represented in 4 m+ o (m) bits. This is …
Relative suffix trees
Suffix trees are one of the most versatile data structures in stringology, with many
applications in bioinformatics. Their main drawback is their size, which can be tens of times …
applications in bioinformatics. Their main drawback is their size, which can be tens of times …
RLZAP: relative Lempel-Ziv with adaptive pointers
Abstract Relative Lempel-Ziv (RLZ) is a popular algorithm for compressing databases of
genomes from individuals of the same species when fast random access is desired. With …
genomes from individuals of the same species when fast random access is desired. With …
Compressed spaced suffix arrays
As a first step in designing relatively-compressed data structures—ie, such that storing an
instance for one dataset helps us store instances for similar datasets—we consider how to …
instance for one dataset helps us store instances for similar datasets—we consider how to …
[PDF][PDF] Relative compressed suffix trees
Suffix trees are one of the most versatile data structures in stringology, with many
applications in bioinformatics. Their main drawback is their size, which can be tens of times …
applications in bioinformatics. Their main drawback is their size, which can be tens of times …
Succinct de Bruijn Graphs (圧縮de Bruijn グラフ)
アレクサンダーボウ - ir.soken.ac.jp
While consumer-grade genotyping–such as that used by 23andMe–has proven a popular
and inexpensive method to determine Single Nucleotide Polymorphisms (SNPs) in …
and inexpensive method to determine Single Nucleotide Polymorphisms (SNPs) in …