|Title||PanTools: representation, storage and exploration of pan-genomic data|
|Author(s)||Sheikhizadeh Anari, S.; Schranz, M.E.; Akdel, Mehmet; Ridder, D. de; Smit, S.|
|Source||Bioinformatics 32 (2016)17. - ISSN 1367-4803 - p. i487 - i493.|
|Event||ECCB 2016, The Hague, 2016-09-03/2016-09-07|
|Publication type||Refereed Article in a scientific journal|
|Abstract||Motivation: 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 pangenome 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.
Results: 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.
Availability and Implementation: The Java implementation of PanTools is publicly available at http://www.bif.wur.nl.