Bahar Alipanahi1, Alan Kuhnle2, Simon J Puglisi3, Leena Salmela3, Christina Boucher1. 1. Department of Computer and Information Science and Engineering, College of Engineering, University of Florida, Gainesville, FL 32611, USA. 2. Department of Computer Science, Florida State University, Tallahassee, FL 32306, USA. 3. Department of Computer Science, Helsinki Institute for Information Technology, University of Helsinki, Helsinki 00014, Finland.
Abstract
MOTIVATION: The de Bruijn graph is one of the fundamental data structures for analysis of high throughput sequencing data. In order to be applicable to population-scale studies, it is essential to build and store the graph in a space- and time-efficient manner. In addition, due to the ever-changing nature of population studies, it has become essential to update the graph after construction, e.g. add and remove nodes and edges. Although there has been substantial effort on making the construction and storage of the graph efficient, there is a limited amount of work in building the graph in an efficient and mutable manner. Hence, most space efficient data structures require complete reconstruction of the graph in order to add or remove edges or nodes. RESULTS: In this article, we present DynamicBOSS, a succinct representation of the de Bruijn graph that allows for an unlimited number of additions and deletions of nodes and edges. We compare our method with other competing methods and demonstrate that DynamicBOSS is the only method that supports both addition and deletion and is applicable to very large samples (e.g. greater than 15 billion k-mers). Competing dynamic methods, e.g. FDBG cannot be constructed on large scale datasets, or cannot support both addition and deletion, e.g. BiFrost. AVAILABILITY AND IMPLEMENTATION: DynamicBOSS is publicly available at https://github.com/baharpan/dynboss. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: The de Bruijn graph is one of the fundamental data structures for analysis of high throughput sequencing data. In order to be applicable to population-scale studies, it is essential to build and store the graph in a space- and time-efficient manner. In addition, due to the ever-changing nature of population studies, it has become essential to update the graph after construction, e.g. add and remove nodes and edges. Although there has been substantial effort on making the construction and storage of the graph efficient, there is a limited amount of work in building the graph in an efficient and mutable manner. Hence, most space efficient data structures require complete reconstruction of the graph in order to add or remove edges or nodes. RESULTS: In this article, we present DynamicBOSS, a succinct representation of the de Bruijn graph that allows for an unlimited number of additions and deletions of nodes and edges. We compare our method with other competing methods and demonstrate that DynamicBOSS is the only method that supports both addition and deletion and is applicable to very large samples (e.g. greater than 15 billion k-mers). Competing dynamic methods, e.g. FDBG cannot be constructed on large scale datasets, or cannot support both addition and deletion, e.g. BiFrost. AVAILABILITY AND IMPLEMENTATION: DynamicBOSS is publicly available at https://github.com/baharpan/dynboss. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Jared T Simpson; Kim Wong; Shaun D Jackman; Jacqueline E Schein; Steven J M Jones; Inanç Birol Journal: Genome Res Date: 2009-02-27 Impact factor: 9.043
Authors: Prashant Pandey; Fatemeh Almodaresi; Michael A Bender; Michael Ferdman; Rob Johnson; Rob Patro Journal: Cell Syst Date: 2018-06-20 Impact factor: 10.304
Authors: Martin D Muggli; Alexander Bowe; Noelle R Noyes; Paul S Morley; Keith E Belk; Robert Raymond; Travis Gagie; Simon J Puglisi; Christina Boucher Journal: Bioinformatics Date: 2017-10-15 Impact factor: 6.937