[Bioc-devel] New package: FindMyFriends - Comparative microbial genomics

[Thomas Lin Pedersen]

With the release of the new version of Bioconductor I would like to present my new package.

FindMyFriends is an extensible framework for generating and working with comparative microbial genomics data or, as it is often referred to, pangenomes. On the algorithm side, FindMyFriends offers a new approach to grouping genes from microbial genomes using a heuristic that allows for linear scaling of the computational time, as opposed to the quadratic scaling that almost all current tools have. Furthermore it provides a new post processing step for refining gene groups based on the flanking genes of each member of the group. Completely novel is a set of algorithm that works on a graph representation of the pangenome to identify chromosomal areas of high plasticity, such as insertion/deletion sites, frameshift events etc.

On the infrastructure side FindMyFriends supply an extensible class hierarchy that support annotation of gene groups, secondary grouping of groups, transparent link between groups and underlying raw data, numerous plot functions etc. Currently classes exist to deal with in-memory sequence data as well as sequences stored in fasta files, but due to way the classes are defined it is possible to extent it with classes that support any backend e.g. different databases…

I hope those of you working within microbial genomics will find it useful.

Best

Thomas Lin Pedersen, Technical University of Denmark