UNLABELLED: A typical prokaryote population sequencing study can now consist of hundreds or thousands of isolates. Interrogating these datasets can provide detailed insights into the genetic structure of prokaryotic genomes. We introduce Roary, a tool that rapidly builds large-scale pan genomes, identifying the core and accessory genes. Roary makes construction of the pan genome of thousands of prokaryote samples possible on a standard desktop without compromising on the accuracy of results. Using a single CPU Roary can produce a pan genome consisting of 1000 isolates in 4.5 hours using 13 GB of RAM, with further speedups possible using multiple processors. AVAILABILITY AND IMPLEMENTATION: Roary is implemented in Perl and is freely available under an open source GPLv3 license from http://sanger-pathogens.github.io/Roary CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUMMARY: Multi-locus sequence typing (MLST) is a widely used method of characterization of bacterial isolates. It has been applied to over 50,000 isolates in over 50 different species. Here, we present a coalescent method to jointly simulate MLST data and the clonal genealogy that gave rise to the sample. AVAILABILITY AND IMPLEMENTATION: SimMLST was implemented in C++ and Qt4 for the graphical user interface. It is distributed under the terms of the GNU General Public License. Source code and binaries for Windows and Linux are available from (http://go.warwick.ac.uk/SimMLST). A user guide and a technical description of the algorithm are provided with the program.