PanTools v3: functional annotation, classification and phylogenomics

E.M. Jonkheer; F.J.M. van Workum; S. Sheikhizadeh Anari; B. Brankovics; J.R. de Haan; Lidija Berke; T.A.J. van der Lee; D. de Ridder; S. Smit

doi:10.1093/bioinformatics/btac506

PanTools v3: functional annotation, classification and phylogenomics

E.M. Jonkheer^*, F.J.M. van Workum, S. Sheikhizadeh Anari, B. Brankovics, J.R. de Haan, Lidija Berke, T.A.J. van der Lee, D. de Ridder, S. Smit^*

^*Corresponding author for this work

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

12 Citations (Scopus)

Abstract

The ever-increasing number of sequenced genomes necessitates the development of pangenomic approaches for comparative genomics. Introduced in 2016, PanTools is a platform that allows pangenome construction, homology grouping and pangenomic read mapping. The use of graph database technology makes PanTools versatile, applicable from small viral genomes like SARS-CoV-2 up to large plant or animal genomes like tomato or human. Here, we present our third major update to PanTools that enables the integration of functional annotations and provides both gene-level analyses and phylogenetics.

Original language	English
Pages (from-to)	4403-4405
Journal	Bioinformatics
Volume	38
Issue number	18
DOIs	https://doi.org/10.1093/bioinformatics/btac506
Publication status	Published - 15 Sept 2022

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10.1093/bioinformatics/btac506Licence: CC BY

https://edepot.wur.nl/580443Licence: CC BY

Data underlying the publication: "PanTools v3: functional annotation, classification, and phylogenomics "
Jonkheer, E. (Creator) & Smit, S. (Creator), Wageningen University & Research, 4 Jul 2022
DOI: 10.4121/19874485
Dataset

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AU - Jonkheer, E.M.

AU - van Workum, F.J.M.

AU - Sheikhizadeh Anari, S.

AU - Brankovics, B.

AU - de Haan, J.R.

AU - Berke, Lidija

AU - van der Lee, T.A.J.

AU - de Ridder, D.

AU - Smit, S.

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AB - The ever-increasing number of sequenced genomes necessitates the development of pangenomic approaches for comparative genomics. Introduced in 2016, PanTools is a platform that allows pangenome construction, homology grouping and pangenomic read mapping. The use of graph database technology makes PanTools versatile, applicable from small viral genomes like SARS-CoV-2 up to large plant or animal genomes like tomato or human. Here, we present our third major update to PanTools that enables the integration of functional annotations and provides both gene-level analyses and phylogenetics.

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PanTools v3: functional annotation, classification and phylogenomics

Abstract

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Data underlying the publication: "PanTools v3: functional annotation, classification, and phylogenomics "

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