Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs

Guillaume Holley,Páll Melsted

doi:10.1186/s13059-020-02135-8

Abstract

Memory consumption of de Bruijn graphs is often prohibitive. Most de Bruijn graph-based assemblers reduce the complexity by compacting paths into single vertices, but this is challenging as it requires the uncompacted de Bruijn graph to be available in memory. We present a parallel and memory-efficient algorithm enabling the direct construction of the compacted de Bruijn graph without producing the intermediate uncompacted graph. Bifrost features a broad range of functions, such as indexing, editing, and querying the graph, and includes a graph coloring method that maps each k-mer of the graph to the genomes it occurs in.Availabilityhttps://github.com/pmelsted/bifrost

Highlights

The de Bruijn graph is an abstract data structure with a rich history in computational biology as a tool for genome assembly [1, 2]
We focus on tools for constructing compacted de Bruijn graphs with or without colors
We focus on three representative use cases: compacted de Bruijn graphs (cdBGs) construction, cdBG querying, and cdBG coloring

Summary

Introduction

The de Bruijn graph is an abstract data structure with a rich history in computational biology as a tool for genome assembly [1, 2]. With the advent of high throughput sequencing, the Overlap Layout Consensus (OLC) framework frequently used to assemble Sanger sequencing data [3] was progressively replaced in favor of de Bruijn graph-based methods. De Bruijn graphs have found widespread use for a variety of problems such as de novo transcriptome assembly [19], variant calling [20], short read compression [21], short read correction [22], long read correction [17], and short read mapping [23] to name a few. The initial application was for assembly and genotyping, but it has found use in pan-genomics [25], variant calling [26], and transcript quantification methods [27]

Results

Discussion

Conclusion