TwoPaCo: An efficient algorithm to build the compacted de Bruijn graph from many complete genomes

TL;DR

TwoPaCo is a scalable, low-memory algorithm that efficiently constructs compacted de Bruijn graphs from large sets of complete genomes, enabling advanced genomic analyses.

Contribution

It introduces a novel algorithm capable of building the compacted de Bruijn graph from many large genomes quickly and with low memory usage.

Findings

Constructs graphs for 100 simulated human genomes in less than a day.

Builds graphs for eight primate genomes in under two hours.

Enables analysis of hundreds of mammalian genomes.

Abstract

Motivation: De Bruijn graphs have been proposed as a data structure to facilitate the analysis of related whole genome sequences, in both a population and comparative genomic settings. However, current approaches do not scale well to many genomes of large size (such as mammalian genomes). Results: In this paper, we present TwoPaCo, a simple and scalable low memory algorithm for the direct construction of the compacted de Bruijn graph from a set of complete genomes. We demonstrate that it can construct the graph for 100 simulated human genomes in less then a day and eight real primates in less than two hours, on a typical shared-memory machine. We believe that this progress will enable novel biological analyses of hundreds of mammalian-sized genomes. Availability: Our code and data is available for download from github.com/medvedevgroup/TwoPaCo Contact: ium125@psu.edu