Socru: Typing of genome level order and orientation in bacteria

Abstract

SummaryGenome rearrangements occur in bacteria between repeat sequences and impact growth and gene expression. Homologous recombination can occur between ribosomal operons, which are found in multiple copies in many bacteria. Inversion between indirect repeats and excision/translocation between direct repeats enable structural genome rearrangement. To identify what these rearrangements are by sequencing, reads of several thousand bases are required to span the ribosomal operons. With long read sequencing aiding the routine generation of complete bacterial assemblies, we have developed socru, a typing method for the order and orientation of genome fragments between ribosomal operons, defined against species-specific baselines. It allows for a single identifier to convey the order and orientation of genome level structure and 434 of the most common bacterial species are supported. Additionally, socru can be used to identify large scale misassemblies. Availability and implementationSocru is written in Python 3, runs on Linux and OSX systems and is available under the open source license GNU GPL 3 from https://github.com/quadram-institute-bioscience/socru. Contactgemma.langridge@quadram.ac.uk