Simurg is an R package to simulate bacterial pangenomes under different evolutionary constraints. It is intended to produce simulated pangenomes using reference sequences as starting point from a Most Recent Common Ancestor (MRCA), on the Neutral and Infinitely Many Genes (IMG) model that produce changes (gene gain/loss) along branches of a simulated coalescent tree.
Porefile is a Nextflow pipeline that wraps a bunch of third-party software to process and classify full-length 16S (SSU) sequences generated using the long-read sequencing platforms from Oxford Nanopore Technologies. Users can select among a set of sub-workflows implemented, or all at once. Each sub-workflow uses different software to align ONT amplicon reads against the SILVA SSU NR99 database, which is downloaded on the fly if not provided by the user. Reads are then classified by MEGAN6 CE tools, and using a SILVA-to-NCBI accession mapping file provided by MEGAN authors, which is also downloaded on the fly if not provided by the user.
MLSTar is an R package that allows to easily determine the Multi-Locus Sequence Type (MLST) of your genomes. It also works as an interface between PubMLST through their RESTful API, so you don’t have to bother downloading and collecting files: the application does it automatically. Today the package works in Unix-based systems.
Pagoo is an encapsulated, object-oriented class system for analyzing bacterial pangenomes. It uses the R6 package as backend. It was designed in order to facilitate and speed-up the comparative analysis of multiple bacterial genomes, standardizing and optimizing tasks performed routinely. There are a handful of things done everyday when working with bacterial pangenomes: subset, summarize, extract, visualize and store data. So, Pagoo is intended to facilitate these tasks as much as possible.