Efficient construction of the extended BWT from grammar-compressed DNA sequencing reads

We present an algorithm for building the extended BWT (eBWT) of a string collection from its grammar-compressed representation. Our technique exploits the string repetitions captured by the grammar to boost the computation of the eBWT. Thus, the more repetitive the collection is, the lower are the r...

Full description

Saved in:
Bibliographic Details
Published in:arXiv.org 2021-02
Main Author: Diego Diaz-Dominguez annd Gonzalo Navarro
Format: Article
Language:English
Subjects:
Algorithms
Bioinformatics
Construction
Gene sequencing
Strings
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:We present an algorithm for building the extended BWT (eBWT) of a string collection from its grammar-compressed representation. Our technique exploits the string repetitions captured by the grammar to boost the computation of the eBWT. Thus, the more repetitive the collection is, the lower are the resources we use per input symbol. We rely on a new grammar recently proposed at DCC'21 whose nonterminals serve as building blocks for inducing the eBWT. A relevant application for this idea is the construction of self-indexes for analyzing sequencing reads -- massive and repetitive string collections of raw genomic data. Self-indexes have become increasingly popular in Bioinformatics as they can encode more information in less space. Our efficient eBWT construction opens the door to perform accurate bioinformatic analyses on more massive sequence datasets, which are not tractable with current eBWT construction techniques.
ISSN:2331-8422