deltaRpkm: an R package for a rapid detection of differential gene presence between related bacterial genomes.

Akarsu, Hatice; Aguilar-Bultet, Lisandra; Falquet, Laurent (2019). deltaRpkm: an R package for a rapid detection of differential gene presence between related bacterial genomes. BMC bioinformatics, 20(1), p. 621. BioMed Central 10.1186/s12859-019-3234-2

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Comparative genomics has seen the development of many software performing the clustering, polymorphism and gene content analysis of genomes at different phylogenetic levels (isolates, species). These tools rely on de novo assembly and/or multiple alignments that can be computationally intensive for large datasets. With a large number of similar genomes in particular, e.g., in surveillance and outbreak detection, assembling each genome can become a redundant and expensive step in the identification of genes potentially involved in a given clinical feature.


We have developed deltaRpkm, an R package that performs a rapid differential gene presence evaluation between two large groups of closely related genomes. Starting from a standard gene count table, deltaRpkm computes the RPKM per gene per sample, then the inter-group δRPKM values, the corresponding median δRPKM (m) for each gene and the global standard deviation value of m (sm). Genes with m >  = 2 ∗ sm (standard deviation s of all the m values) are considered as "differentially present" in the reference genome group. Our simple yet effective method of differential RPKM has been successfully applied in a recent study published by our group (N = 225 genomes of Listeria monocytogenes) (Aguilar-Bultet et al. Front Cell Infect Microbiol 8:20, 2018).


To our knowledge, deltaRpkm is the first tool to propose a straightforward inter-group differential gene presence analysis with large datasets of related genomes, including non-coding genes, and to output directly a list of genes potentially involved in a phenotype.

Item Type:

Journal Article (Original Article)


05 Veterinary Medicine > Research Foci > Host-Pathogen Interaction
05 Veterinary Medicine > Department of Infectious Diseases and Pathobiology (DIP) > Institute of Veterinary Bacteriology

Graduate School:

Graduate School for Cellular and Biomedical Sciences (GCB)

UniBE Contributor:

Aguilar Bultet, Lisandra


500 Science > 570 Life sciences; biology
600 Technology > 630 Agriculture




BioMed Central




Pamela Schumacher

Date Deposited:

02 Apr 2020 09:43

Last Modified:

05 Dec 2022 15:37

Publisher DOI:


PubMed ID:


Uncontrolled Keywords:

Comparative genomics Differential gene presence/absence RPKM




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