title: PanTools: representation, storage and exploration of pan-genomic data.
abstract: Next-generation sequencing technology is generating a wealth of highly similar genome sequences for many species, paving the way for a transition from single-genome to pan-genome analyses. Accordingly, genomics research is going to switch from reference-centric to pan-genomic approaches. We define the pan-genome as a comprehensive representation of multiple annotated genomes, facilitating analyses on the similarity and divergence of the constituent genomes at the nucleotide, gene and genome structure level. Current pan-genomic approaches do not thoroughly address scalability, functionality and usability.
  
  
  
  We introduce a generalized De Bruijn graph as a pan-genome representation, as well as an online algorithm to construct it. This representation is stored in a Neo4j graph database, which makes our approach scalable to large eukaryotic genomes. Besides the construction algorithm, our software package, called PanTools, currently provides functionality for annotating pan-genomes, adding sequences, grouping genes, retrieving gene sequences or genomic regions, reconstructing genomes and comparing and querying pan-genomes. We demonstrate the performance of the tool using datasets of 62 E. coli genomes, 93 yeast genomes and 19 Arabidopsis thaliana genomes.
  
  
  
  The Java implementation of PanTools is publicly available at http://www.bif.wur.nl
  
  
  
  sandra.smit@wur.nl.
authors: Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
authors: Siavash
authors: S
authors: Sheikhizadeh
authors: Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, The Netherlands.
authors: M Eric
authors: ME
authors: Schranz
authors: Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
authors: Mehmet
authors: M
authors: Akdel
authors: Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
authors: Dick
authors: D
authors: de Ridder
authors: Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
authors: Sandra
authors: S
authors: Smit
mesh_terms: D000465:Algorithms; D017360:Arabidopsis; D019295:Computational Biology / Q000379:methods; D004926:Escherichia coli; D016678:Genome; D016680:Genome, Bacterial; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D012984:Software