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

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 Sep 2022

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title = "PanTools v3: functional annotation, classification and phylogenomics",

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.",

author = "E.M. Jonkheer and {van Workum}, F.J.M. and {Sheikhizadeh Anari}, S. and B. Brankovics and {de Haan}, J.R. and Lidija Berke and {van der Lee}, T.A.J. and {de Ridder}, D. and S. Smit",

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doi = "10.1093/bioinformatics/btac506",

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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.

PY - 2022/9/15

Y1 - 2022/9/15

N2 - 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.

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.

U2 - 10.1093/bioinformatics/btac506

DO - 10.1093/bioinformatics/btac506

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SP - 4403

EP - 4405

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 18

ER -

PanTools v3: functional annotation, classification and phylogenomics

Abstract

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