PanTools: representation, storage and exploration of pan-genomic data

S. Sheikhizadeh Anari; M.E. Schranz; Mehmet Akdel; D. de Ridder; S. Smit

doi:10.1093/bioinformatics/btw455

PanTools: representation, storage and exploration of pan-genomic data

S. Sheikhizadeh Anari, M.E. Schranz, Mehmet Akdel, D. de Ridder, S. Smit^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

39 Citations (Scopus)

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: [email protected]

Original language	English
Pages (from-to)	i487-i493
Journal	Bioinformatics
Volume	32
Issue number	17
DOIs	https://doi.org/10.1093/bioinformatics/btw455
Publication status	Published - 2016
Event	ECCB 2016: The 15th European Conference on Computational Biology - World Forum Convention Center , The Hague, Netherlands Duration: 3 Sept 2016 → 7 Sept 2016 http://www.eccb2016.org

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10.1093/bioinformatics/btw455Licence: CC BY-NC

39 Citations
1 Software

PanTools
Nijveen, H., Smit, S., Medema, M. H., de Ridder, D., van Dijk, A. D. J., Jonkheer, E. M., van der Hooft, J. J. J., van Lankveld, T., Moed, M. & van Workum, F. J. M., 2019
Research output: Non-textual form › Software

Open Access

Cite this

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title = "PanTools: representation, storage and exploration of pan-genomic data",

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 multipleannotated 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: [email protected]",

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T1 - PanTools: representation, storage and exploration of pan-genomic data

AU - Sheikhizadeh Anari, S.

AU - Schranz, M.E.

AU - Akdel, Mehmet

AU - de Ridder, D.

AU - Smit, S.

PY - 2016

Y1 - 2016

N2 - 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 multipleannotated 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: [email protected]

AB - 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 multipleannotated 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: [email protected]

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DO - 10.1093/bioinformatics/btw455

M3 - Article

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JO - Bioinformatics

JF - Bioinformatics

IS - 17

T2 - ECCB 2016

Y2 - 3 September 2016 through 7 September 2016

ER -

PanTools: representation, storage and exploration of pan-genomic data

Abstract

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Research output

PanTools

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