title: Robust high-throughput prokaryotede novoassembly and improvement pipeline for Illumina data.
abstract: The rapidly reducing cost of bacterial genome sequencing has lead to its routine use in large-scale microbial analysis. Though mapping approaches can be used to find differences relative to the reference, many bacteria are subject to constant evolutionary pressures resulting in events such as the loss and gain of mobile genetic elements, horizontal gene transfer through recombination and genomic rearrangements.De novoassembly is the reconstruction of the underlying genome sequence, an essential step to understanding bacterial genome diversity. Here we present a high-throughput bacterial assembly and improvement pipeline that has been used to generate nearly 20 000 annotated draft genome assemblies in public databases. We demonstrate its performance on a public data set of 9404 genomes. We find all the genes used in multi-locus sequence typing schema present in 99.6 % of assembled genomes. When tested on low-, neutral- and high-GC organisms, more than 94 % of genes were present and completely intact. The pipeline has been proven to be scalable and robust with a wide variety of datasets without requiring human intervention. All of the software is available on GitHub under the GNU GPL open source license.
authors.affiliation: 1​Pathogen Informatics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridgeshire, UK.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Page
authors.affiliation: 1​Pathogen Informatics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridgeshire, UK.
authors.forename: Nishadi
authors.initials: N
authors.lastname: De Silva
authors.affiliation: 1​Pathogen Informatics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridgeshire, UK.
authors.forename: Martin
authors.initials: M
authors.lastname: Hunt
authors.affiliation: 2​Biochemical Development, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridgeshire, UK.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Quail
authors.affiliation: 3​Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridgeshire, UK.
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.affiliation: 3​Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridgeshire, UK.
authors.forename: Simon R
authors.initials: SR
authors.lastname: Harris
authors.affiliation: 4​Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridgeshire, UK.
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Otto
authors.affiliation: 1​Pathogen Informatics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridgeshire, UK.
authors.forename: Jacqueline A
authors.initials: JA
authors.lastname: Keane
mesh_terms: D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics / Q000191:economics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D058885:Multilocus Sequence Typing; D011387:Prokaryotic Cells; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
keywords: assembly; high-throughput; illumina; prokaryotic