Gsufsort: constructing suffix arrays, LCP arrays and BWTs for string collections.

ABSTRACT:

Background

The construction of a suffix array for a collection of strings is a fundamental task in Bioinformatics and in many other applications that process strings. Related data structures, as the Longest Common Prefix array, the Burrows-Wheeler transform, and the document array, are often needed to accompany the suffix array to efficiently solve a wide variety of problems. While several algorithms have been proposed to construct the suffix array for a single string, less emphasis has been put on algorithms to construct suffix arrays for string collections.

Result

In this paper we introduce gsufsort, an open source software for constructing the suffix array and related data indexing structures for a string collection with N symbols in O(N) time. Our to

SUBMITTER: Louza FA 

PROVIDER: S-EPMC7507297 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature