Metagenome SNP calling via read-colored de Bruijn graphs

Graphite: painting genomes using a colored de Bruijn graph

The recent growth of microbial sequence data allows comparisons at unprecedented scales, enabling the tracking of strains, mobile genetic elements, or genes. Querying a genome against a large reference database can easily yield thousands of matches that are tedious to interpret and pose computational challenges. We developed Graphite that uses a colored de Bruijn graph (cDBG) to paint query genomes, selecting the local best matches along the full query length. By focusing on the best genomic match of each query region, Graphite reduces the number of matches while providing the most promising leads for sequence tracking or genomic forensics. When applied to hundreds of Campylobacter genomes we found extensive gene sharing, including a previously undetected C. coli plasmid that matched a C. jejuni chromosome. Together, genome painting using cDBGs as enabled by Graphite, can reveal new biological phenomena by mitigating computational hurdles.

Applications of de Bruijn graphs in microbiome research

High-throughput sequencing has become an increasingly central component of microbiome research. The development of de Bruijn graph-based methods for assembling high-throughput sequencing data has been an important part of the broader adoption of sequencing as part of biological studies. Recent advances in the construction and representation of de Bruijn graphs have led to new approaches that utilize the de Bruijn graph data structure to aid in different biological analyses. One type of application of these methods has been in alternative approaches to the assembly of sequencing data like gene-targeted assembly, where only gene sequences are assembled out of larger metagenomes, and differential assembly, where sequences that are differentially present between two samples are assembled. de Bruijn graphs have also been applied for comparative genomics where they can be used to represent large sets of multiple genomes or metagenomes where structural features in the graphs can be used to identify variants, indels, and homologous regions in sequences. These de Bruijn graph-based representations of sequencing data have even begun to be applied to whole sequencing databases for large-scale searches and experiment discovery. de Bruijn graphs have played a central role in how high-throughput sequencing data is worked with, and the rapid development of new tools that rely on these data structures suggests that they will continue to play an important role in biology in the future.

Buffering updates enables efficient dynamic de Bruijn graphs

MOTIVATION

The de Bruijn graph has become a ubiquitous graph model for biological data ever since its initial introduction in the late 1990s. It has been used for a variety of purposes including genome assembly (Zerbino and Birney, 2008; Bankevich et al., 2012; Peng et al., 2012), variant detection (Alipanahi et al., 2020b; Iqbal et al., 2012), and storage of assembled genomes (Chikhi et al., 2016). For this reason, there have been over a dozen methods for building and representing the de Bruijn graph and its variants in a space and time efficient manner.

RESULTS

With the exception of a few data structures (Muggli et al., 2019; Holley and Melsted, 2020; Crawford et al.,2018), compressed and compact de Bruijn graphs do not allow for the graph to be efficiently updated, meaning that data can be added or deleted. The most recent compressed dynamic de Bruijn graph (Alipanahi et al., 2020a), relies on dynamic bit vectors which are slow in theory and practice. To address this shortcoming, we present a compressed dynamic de Bruijn graph that removes the necessity of dynamic bit vectors by buffering data that should be added or removed from the graph. We implement our method, which we refer to as BufBOSS, and compare its performance to Bifrost, DynamicBOSS, and FDBG. Our experiments demonstrate that BufBOSS achieves attractive trade-offs compared to other tools in terms of time, memory and disk, and has the best deletion performance by an order of magnitude.

Sparse Binary Relation Representations for Genome Graph Annotation

High-throughput DNA sequencing data are accumulating in public repositories, and efficient approaches for storing and indexing such data are in high demand. In recent research, several graph data structures have been proposed to represent large sets of sequencing data and to allow for efficient querying of sequences. In particular, the concept of labeled de Bruijn graphs has been explored by several groups. Although there has been good progress toward representing the sequence graph in small space, methods for storing a set of labels on top of such graphs are still not sufficiently explored. It is also currently not clear how characteristics of the input data, such as the sparsity and correlations of labels, can help to inform the choice of method to compress the graph labeling. In this study, we present a new compression approach, Multi-binary relation wavelet tree (BRWT), which is adaptive to different kinds of input data. We show an up to 29% improvement in compression performance over the basic BRWT method, and up to a 68% improvement over the current state-of-the-art for de Bruijn graph label compression. To put our results into perspective, we present a systematic analysis of five different state-of-the-art annotation compression schemes, evaluate key metrics on both artificial and real-world data, and discuss how different data characteristics influence the compression performance. We show that the improvements of our new method can be robustly reproduced for different representative real-world data sets.