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arXiv · 1602.05856

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

Ilia Minkin·Son Pham·Paul Medvedev
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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

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Ilia Minkin, Son Pham, Paul Medvedev. 2016-02-18. TwoPaCo: An efficient algorithm to build the compacted de Bruijn graph from many complete genomes. https://arxiv.org/abs/1602.05856

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