Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 507416
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
DOI http://dx.doi.org/10.1093/bioinformatics/btw455
Department(s) Bioinformatics
Biosystematics
EPS
Publication type Refereed Article in a scientific journal
Publication year 2016
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.
Contact: sandra.smit@wur.nl
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