title: In SilicoWhole Genome Sequencer and Analyzer (iWGS): a Computational Pipeline to Guide the Design and Analysis ofde novoGenome Sequencing Studies.
abstract: The availability of genomes across the tree of life is highly biased toward vertebrates, pathogens, human disease models, and organisms with relatively small and simple genomes. Recent progress in genomics has enabled thede novodecoding of the genome of virtually any organism, greatly expanding its potential for understanding the biology and evolution of the full spectrum of biodiversity. The increasing diversity of sequencing technologies, assays, andde novoassembly algorithms have augmented the complexity ofde novogenome sequencing projects in nonmodel organisms. To reduce the costs and challenges inde novogenome sequencing projects and streamline their experimental design and analysis, we developed iWGS (in silicoWholeGenomeSequencer and Analyzer), an automated pipeline for guiding the choice of appropriate sequencing strategy and assembly protocols. iWGS seamlessly integrates the four key steps of ade novogenome sequencing project: data generation (through simulation), data quality control,de novoassembly, and assembly evaluation and validation. The last three steps can also be applied to the analysis of real data. iWGS is designed to enable the user to have great flexibility in testing the range of experimental designs available for genome sequencing projects, and supports all major sequencing technologies and popular assembly tools. Three case studies illustrate how iWGS can guide the design ofde novogenome sequencing projects, and evaluate the performance of a wide variety of user-specified sequencing strategies and assembly protocols on genomes of differing architectures. iWGS, along with a detailed documentation, is freely available at https://github.com/zhouxiaofan1983/iWGS.
authors.affiliation: Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235.
authors.forename: Xiaofan
authors.identifier: http://orcid.org/0000-0002-2879-6317
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Laboratory of Genetics, Genome Center of Wisconsin, Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Wisconsin 53706.
authors.forename: David
authors.identifier: http://orcid.org/0000-0001-9912-8802
authors.initials: D
authors.lastname: Peris
authors.affiliation: Laboratory of Genetics, Genome Center of Wisconsin, Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Wisconsin 53706.
authors.forename: Jacek
authors.identifier: http://orcid.org/0000-0002-1916-0122
authors.initials: J
authors.lastname: Kominek
authors.affiliation: Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, Illinois 61604.
authors.forename: Cletus P
authors.identifier: http://orcid.org/0000-0002-2208-9814
authors.initials: CP
authors.lastname: Kurtzman
authors.affiliation: Laboratory of Genetics, Genome Center of Wisconsin, Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Wisconsin 53706 cthittinger@wisc.edu antonis.rokas@vanderbilt.edu.
authors.forename: Chris Todd
authors.identifier: http://orcid.org/0000-0001-5088-7461
authors.initials: CT
authors.lastname: Hittinger
authors.affiliation: Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235 cthittinger@wisc.edu antonis.rokas@vanderbilt.edu.
authors.forename: Antonis
authors.identifier: http://orcid.org/0000-0002-7248-6551
authors.initials: A
authors.lastname: Rokas
keywords: de novo assembly; experimental design; genome sequencing; high-throughput sequencing; nonmodel organism; simulation