DeBWT: parallel construction of Burrows-Wheeler Transform for large collection of genomes with de Bruijn-branch encoding.

ABSTRACT:

Motivation

With the development of high-throughput sequencing, the number of assembled genomes continues to rise. It is critical to well organize and index many assembled genomes to promote future genomics studies. Burrows-Wheeler Transform (BWT) is an important data structure of genome indexing, which has many fundamental applications; however, it is still non-trivial to construct BWT for large collection of genomes, especially for highly similar or repetitive genomes. Moreover, the state-of-the-art approaches cannot well support scalable parallel computing owing to their incremental nature, which is a bottleneck to use modern computers to accelerate BWT construction.

Results

We propose de Bruijn branch-based BWT constructor (deBWT), a novel parallel BWT construction approa

SUBMITTER: Liu B 

PROVIDER: S-EPMC4908350 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature