AbstractMotivationThe de Bruijn graph has become a ubiquitous graph model for biological data ever since its initial introduction in the later 1990s. It has been used for a variety of purposes including genome assembly (Zerbino and Birney, 2008; Bankevich et al., 2012b; 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.ResultsAlthough there exists a plethora of space efficient data structures for storing the de Bruijn graph, the majority of them make a compression-mutability trade-off. In particular, with the exception of a few methods (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, allowing for data to 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 BufBOSS which is 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 out of all the tools that are able to perform deletions. Our implementation is available at https://github.com/jnalanko/[email protected]
The Maximum Independent Sets of de Bruijn Graphs of Diameter 3
