Jacqueline A Keane | bioRxiv Science

bioRxiv2015

Circlator: automated circularization of genome assemblies using long sequencing reads

The assembly of DNA sequence data into finished genomes is undergoing a renais-sance thanks to emerging technologies producing reads of tens of kilobases. Assembling complete bacterial and small eukaryotic genomes is now possible, but the final step of circularizing sequences remains unsolved. Here we present Circlator, the first tool to automate assembly circularization and produce accurate linear rep-resentations of circular sequences. Using Pacific Biosciences and Oxford Nanopore data, Circlator correctly circularized 26 of 27 circularizable sequences, comprising 11 chromosomes and 12 plasmids from bacteria, the apicoplast and mitochondrion of Plasmodium falciparum and a human mitochondrion. Circlator is available at http://sanger-pathogens.github.io/circlator/.

Bioinformatics↗

bioRxiv2015

Roary: Rapid large-scale prokaryote pan genome analysis

SummaryA 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 of prokaryotic genomes. We introduce Roary, a tool that rapidly builds large-scale pan genomes, identifying the core and dispensable 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.\n\nAvailability and implementationRoary is implemented in Perl and is freely available under an open source GPLv3 license from http://sanger-pathogens.github.io/Roary\n\nContactroary@sanger.ac.uk\n\nSupplementary informationSupplementary data are available at Bioinformatics online.

Bioinformatics↗