Dataset Information

PanTools v3: functional annotation, classification, and phylogenomics.

ABSTRACT:

Summary

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.

Availability and implementation

PanTools is implemented in Java 8 and released under the GNU GPLv3 license. Software and documentation are available at https://git.wur.nl/bioinformatics/pantools.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Jonkheer EM

PROVIDER: S-EPMC9477522 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature

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Publications

PanTools v3: functional annotation, classification and phylogenomics.

Jonkheer Eef M EM van Workum Dirk-Jan M DM Sheikhizadeh Anari Siavash S Brankovics Balázs B de Haan Jorn R JR Berke Lidija L van der Lee Theo A J TAJ de Ridder Dick D Smit Sandra S

Bioinformatics (Oxford, England) 20220901 18

<h4>Summary</h4>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 ...[more]

PMID: 35861394

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