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

ABSTRACT:

Background

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.

Results

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, deltaR

SUBMITTER: Akarsu H 

PROVIDER: S-EPMC6889214 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature