Dataset Information

The epiGenomic Efficient Correlator (epiGeEC) tool allows fast comparison of user datasets with thousands of public epigenomic datasets.

ABSTRACT:

Summary

In recent years, major initiatives such as the International Human Epigenome Consortium have generated thousands of high-quality genome-wide datasets for a large variety of assays and cell types. This data can be used as a reference to assess whether the signal from a user-provided dataset corresponds to its expected experiment, as well as to help reveal unexpected biological associations. We have developed the epiGenomic Efficient Correlator (epiGeEC) tool to enable genome-wide comparisons of very large numbers of datasets. A public Galaxy implementation of epiGeEC allows comparison of user datasets with thousands of public datasets in a few minutes.

Availability and implementation

The source code is available at https://bitbucket.org/labjacquespe/epigeec and the Galaxy implementation at http://epigeec.genap.ca.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Laperle J

PROVIDER: S-EPMC6378939 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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Publications

The epiGenomic Efficient Correlator (epiGeEC) tool allows fast comparison of user datasets with thousands of public epigenomic datasets.

Laperle Jonathan J Hébert-Deschamps Simon S Raby Joanny J de Lima Morais David A DA Barrette Michel M Bujold David D Bastin Charlotte C Robert Marc-Antoine MA Nadeau Jean-François JF Harel Marie M Nordell-Markovits Alexei A Veilleux Alain A Bourque Guillaume G Jacques Pierre-Étienne PÉ

Bioinformatics (Oxford, England) 20190201 4

<h4>Summary</h4>In recent years, major initiatives such as the International Human Epigenome Consortium have generated thousands of high-quality genome-wide datasets for a large variety of assays and cell types. This data can be used as a reference to assess whether the signal from a user-provided dataset corresponds to its expected experiment, as well as to help reveal unexpected biological associations. We have developed the epiGenomic Efficient Correlator (epiGeEC) tool to enable genome-wide ...[more]

PMID: 30052804

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Project description:BackgroundContinued sequencing efforts coupled with advances in sequencing technology will lead to the completion of a vast number of small genomes. Whole-genome comparisons represent an important part of the analysis of any new genome sequence, as they can provide a better understanding of the biology and evolution of the source organism. Visualization of the results is important, as it allows information from a variety of sources to be integrated and interpreted. However, existing graphical comparison tools lack features needed for efficiently comparing a new genome to hundreds or thousands of existing sequences. Moreover, existing tools are limited in terms of the types of comparisons that can be performed, the extent to which the output can be customized, and the ease with which the entire process can be automated.ResultsThe CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences of interest to existing genomes or sequence collections. The comparisons are conducted using BLAST, and the BLAST results are presented in the form of graphical maps that can also show sequence features, gene and protein names, COG (Clusters of Orthologous Groups of proteins) category assignments, and sequence composition characteristics. CCT can generate maps in a variety of sizes, including 400 Megapixel maps suitable for posters. Comparisons can be conducted within a particular species or genus, or all available genomes can be used. The entire map creation process, from downloading sequences to redrawing zoomed maps, can be completed easily using scripts included with the CCT. User-defined features or analysis results can be included on maps, and maps can be extensively customized. To simplify program setup, a CCT virtual machine that includes all dependencies preinstalled is available. Detailed tutorials illustrating the use of CCT are included with the CCT documentation.ConclusionCCT can be used to visually compare a reference sequence to thousands of existing genomes or sequence collections (next-generation sequencing reads for example) on a standard desktop computer. It provides analysis and visualization functionality not available in any existing circular genome visualization tool. By visually presenting sequence conservation information along with functional classifications and sequence composition characteristics, CCT can be a useful tool for identifying rapidly evolving or novel sequences, horizontally transferred sequences, or unusual functional properties in newly sequenced genomes. CCT is freely available for download at http://stothard.afns.ualberta.ca/downloads/CCT/.

Dataset Information

The epiGenomic Efficient Correlator (epiGeEC) tool allows fast comparison of user datasets with thousands of public epigenomic datasets.

Summary

Availability and implementation

Supplementary information

Publications

The epiGenomic Efficient Correlator (epiGeEC) tool allows fast comparison of user datasets with thousands of public epigenomic datasets.

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