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Integratinglong-rangeconnectivityinformation into deBruijn graphs Isaac TurnerKiran GarimellaZamin Iqbal2018 год

Integrating long-range connectivity information into de Bruijn graphs
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Аннотация: The de Bruijn graph is a simple and efficient data structure that is used in many areas of sequence analysis including genome assembly, read error correction and variant calling. The data structure has a single parameter k, is straightforward to implement and is tractable for large genomes with high sequencing depth. It also enables representation of multiple samples simultaneously to facilitate comparison. However, unlike the string graph, a de Bruijn graph does not retain long range information that is inherent in the read data. For this reason, applications that rely on de Bruijn graphs can produce sub-optimal results given their input data.We present a novel assembly graph data structure: the Linked de Bruijn Graph (LdBG). Constructed by adding annotations on top of a de Bruijn graph, it stores long range connectivity information through the graph. We show that with error-free data it is possible to losslessly store and recover sequence from a Linked de Bruijn graph. With assembly simulations we demonstrate that the LdBG data structure outperforms both our de Bruijn graph and the String Graph Assembler (SGA). Finally we apply the LdBG to Klebsiella pneumoniae short read data to make large (12 kbp) variant calls, which we validate using PacBio sequencing data, and to characterize the genomic context of drug-resistance genes.Linked de Bruijn Graphs and associated algorithms are implemented as part of McCortex, which is available under the MIT license at https://github.com/mcveanlab/mccortex.Supplementary data are available at Bioinformatics online.
Год издания: 2018
Авторы: Isaac Turner, Kiran Garimella, Zamin Iqbal, Gil McVean
Издательство: Oxford University Press
Источник: Bioinformatics
Ключевые слова: Genomics and Phylogenetic Studies, RNA and protein synthesis mechanisms, Microbial Community Ecology and Physiology
Другие ссылки: Bioinformatics (PDF)
Bioinformatics (HTML)
Europe PMC (PubMed Central) (PDF)
Europe PMC (PubMed Central) (HTML)
Oxford University Research Archive (ORA) (University of Oxford) (PDF)
Oxford University Research Archive (ORA) (University of Oxford) (HTML)
PubMed Central (HTML)
bioRxiv (Cold Spring Harbor Laboratory) (HTML)
PubMed (HTML)