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Background  Recently, Marcus et al. (Bioinformatics 30:3476–83,  2014 ) proposed to use a compressed de Bruijn graph to describe the relationship between the genomes of many individuals/strains of the same or closely related species. They devised an    \documentclass[12pt]{minimal} 				\usepackage{amsmath} 				\usepackage{wasysym}  				\usepackage{amsfonts}  				\usepackage{amssymb}  				\usepackage{amsbsy} 				\usepackage{mathrsfs} 				\usepackage{upgreek} 				\setlength{\oddsidemargin}{-69pt} 				\begin{document}$$O(n\log g)$$\end{document}    O  (  n  log  g  )time algorithm called splitMEM that constructs this graph directly (i.e., without using the uncompressed de Bruijn graph) based on a suffix tree, where  n  is the total length of the genomes and  g  is the length of the longest genome. Baier et al. (Bioinformatics 32:497–504,  2016 ) improved their result.    Results  In this paper, we propose a new space-efficient representation of the compressed de Bruijn graph that adds the possibility to search for a pattern (e.g. an allele—a variant form of a gene) within the pan-genome. The ability to search within the pan-genome graph is of utmost importance and is a design goal of pan-genome data structures.

A representation of a compressed de Bruijn graph for pan-genome analysis that enables search