General Information
| Description | Representation, storage and exploration of pan-genomic data |
| Homepage | http://www.bif.wur.nl |
Publications
PanTools: representation, storage and exploration of pan-genomic data
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 pan-genome 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
Related Tools
deBWT
Published June 2016
Parallel construction of Burrows–Wheeler Transform for large collection of genomes with de Bruijn-branch encoding
Hierarchical sets
Published January 2017
Analyzing pangenome structure through scalable set visualizations
PanViz
Published December 2016
Interactive visualization of the structure of functionally annotated pangenomes
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