in silico Whole Genome Sequencer &amp; Analyzer (iWGS): A Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies

Zhou, Xiaofan; Peris, David; Kominek, Jacek; Kurtzman, Cletus P.; Hittinger, Chris Todd; Rokas, A.

doi:10.1534/g3.116.034249

in silico Whole Genome Sequencer & Analyzer (iWGS): A Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies

Journal Article · Fri Sep 16 00:00:00 EDT 2016 · G3

DOI:https://doi.org/10.1534/g3.116.034249· OSTI ID:1373365

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Vanderbilt Univ., Nashville, TN (United States). Dept. of Biological Sciences
Univ. of Wisconsin, Madison, WI (United States). Wisconsin Energy Inst., J. F. Crow Inst. for the Study of Evolution, Lab. of Genetics, Genome Center of Wisconsin, Dept. of Energy Great Lakes Bioenergy Research Center
US Dept. of Agriculture (USDA)., Peoria, IL (United States). National Center for Agricultural Utilization Research, Agricultural Research Service, Mycotoxin Prevention and Applied Microbiology Research Unit

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 the de novo decoding 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, and de novo assembly algorithms have augmented the complexity of de novo genome sequencing projects in nonmodel organisms. To reduce the costs and challenges in de novo genome sequencing projects and streamline their experimental design and analysis, we developed iWGS (in silico Whole Genome Sequencer and Analyzer), an automated pipeline for guiding the choice of appropriate sequencing strategy and assembly protocols. iWGS seamlessly integrates the four key steps of a de novo genome sequencing project: data generation (through simulation), data quality control, de novo assembly, 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 of de novo genome 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.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory-Advanced Photon Source, Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); National Institutes of Health (NIH); National Science Foundation (NSF)

Grant/Contract Number:: AC02-06CH11357; AC02-05CH11231; FC02-07ER64494

OSTI ID:: 1373365

Alternate ID(s):: OSTI ID: 1378364

Journal Information:: G3, Journal Name: G3 Journal Issue: 11 Vol. 6; ISSN 2160-1836

Publisher:: Genetics Society of AmericaCopyright Statement

Country of Publication:: United States

Language:: English

References (80)

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly Koren, Sergey; Phillippy, Adam M. Current Opinion in Microbiology, Vol. 23 https://doi.org/10.1016/j.mib.2014.11.014	journal	February 2015
Mitochondrial inheritance in budding yeasts: towards an integrated understanding Solieri, Lisa Trends in Microbiology, Vol. 18, Issue 11 https://doi.org/10.1016/j.tim.2010.08.001	journal	November 2010
Harnessing genomics for evolutionary insights Rokas, Antonis; Abbot, Patrick Trends in Ecology & Evolution, Vol. 24, Issue 4 https://doi.org/10.1016/j.tree.2008.11.004	journal	April 2009
Genome sequence of the human malaria parasite Plasmodium falciparum Gardner, Malcolm J.; Hall, Neil; Fung, Eula Nature, Vol. 419, Issue 6906 https://doi.org/10.1038/nature01097	journal	October 2002
Genome-scale approaches to resolving incongruence in molecular phylogenies Rokas, Antonis; Williams, Barry L.; King, Nicole Nature, Vol. 425, Issue 6960 https://doi.org/10.1038/nature02053	journal	October 2003
Inferring ancient divergences requires genes with strong phylogenetic signals Salichos, Leonidas; Rokas, Antonis Nature, Vol. 497, Issue 7449 https://doi.org/10.1038/nature12130	journal	May 2013
Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts Otto, Thomas D.; Rayner, Julian C.; Böhme, Ulrike Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms5754	journal	September 2014
Comprehensive variation discovery in single human genomes Weisenfeld, Neil I.; Yin, Shuangye; Sharpe, Ted Nature Genetics, Vol. 46, Issue 12 https://doi.org/10.1038/ng.3121	journal	October 2014
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data Chin, Chen-Shan; Alexander, David H.; Marks, Patrick Nature Methods, Vol. 10, Issue 6 https://doi.org/10.1038/nmeth.2474	journal	May 2013
A complete bacterial genome assembled de novo using only nanopore sequencing data Loman, Nicholas J.; Quick, Joshua; Simpson, Jared T. Nature Methods, Vol. 12, Issue 8 https://doi.org/10.1038/nmeth.3444	journal	June 2015
Sequence assembly demystified Nagarajan, Niranjan; Pop, Mihai Nature Reviews Genetics, Vol. 14, Issue 3 https://doi.org/10.1038/nrg3367	journal	January 2013
DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies Ye, Chengxi; Hill, Christopher M.; Wu, Shigang Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep31900	journal	August 2016
Mutation rates in mammalian genomes Kumar, S.; Subramanian, S. Proceedings of the National Academy of Sciences, Vol. 99, Issue 2 https://doi.org/10.1073/pnas.022629899	journal	January 2002
High-quality draft assemblies of mammalian genomes from massively parallel sequence data Gnerre, S.; MacCallum, I.; Przybylski, D. Proceedings of the National Academy of Sciences, Vol. 108, Issue 4 https://doi.org/10.1073/pnas.1017351108	journal	December 2010
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry Journal of Computational Biology, Vol. 19, Issue 5 https://doi.org/10.1089/cmb.2012.0021	journal	May 2012
ART: a next-generation sequencing read simulator Huang, Weichun; Li, Leping; Myers, Jason R. Bioinformatics, Vol. 28, Issue 4 https://doi.org/10.1093/bioinformatics/btr708	journal	December 2011
pIRS: Profile-based Illumina pair-end reads simulator Hu, Xuesong; Yuan, Jianying; Shi, Yujian Bioinformatics, Vol. 28, Issue 11 https://doi.org/10.1093/bioinformatics/bts187	journal	April 2012
PBSIM: PacBio reads simulator—toward accurate genome assembly Ono, Yukiteru; Asai, Kiyoshi; Hamada, Michiaki Bioinformatics, Vol. 29, Issue 1 https://doi.org/10.1093/bioinformatics/bts649	journal	November 2012
QUAST: quality assessment tool for genome assemblies Gurevich, Alexey; Saveliev, Vladislav; Vyahhi, Nikolay Bioinformatics, Vol. 29, Issue 8 https://doi.org/10.1093/bioinformatics/btt086	journal	February 2013
GAGE-B: an evaluation of genome assemblers for bacterial organisms Magoc, Tanja; Pabinger, Stephan; Canzar, Stefan Bioinformatics, Vol. 29, Issue 14 https://doi.org/10.1093/bioinformatics/btt273	journal	May 2013
The MaSuRCA genome assembler Zimin, Aleksey V.; Marçais, Guillaume; Puiu, Daniela Bioinformatics, Vol. 29, Issue 21 https://doi.org/10.1093/bioinformatics/btt476	journal	August 2013
Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences Utturkar, Sagar M.; Klingeman, Dawn M.; Land, Miriam L. Bioinformatics, Vol. 30, Issue 19 https://doi.org/10.1093/bioinformatics/btu391	journal	June 2014
RAMPART: a workflow management system for de novo genome assembly Mapleson, Daniel; Drou, Nizar; Swarbreck, David Bioinformatics, Vol. 31, Issue 11 https://doi.org/10.1093/bioinformatics/btv056	journal	January 2015
Mitochondrial genome evolution in yeasts: an all-encompassing view Freel, Kelle C.; Friedrich, Anne; Schacherer, Joseph FEMS Yeast Research, Vol. 15, Issue 4 https://doi.org/10.1093/femsyr/fov023	journal	May 2015
Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species Karl, Stephen Journal of Heredity, Vol. 100, Issue 6, p. 659-674 https://doi.org/10.1093/jhered/esp086	journal	November 2009
Simulation of Genome-Wide Evolution under Heterogeneous Substitution Models and Complex Multispecies Coalescent Histories Arenas, Miguel; Posada, David Molecular Biology and Evolution, Vol. 31, Issue 5 https://doi.org/10.1093/molbev/msu078	journal	March 2014
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification Reddy, T. B. K.; Thomas, Alex D.; Stamatis, Dimitri Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku950	journal	October 2014
Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage Chakraborty, Mahul; Baldwin-Brown, James G.; Long, Anthony D. Nucleic Acids Research https://doi.org/10.1093/nar/gkw654	journal	July 2016
Metassembler: Merging and optimizing de novo genome assemblies Wences, Alejandro Hernandez; Schatz, Michel C. Genome Biology https://doi.org/10.1101/016352	journal	March 2015
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs Zerbino, D. R.; Birney, E. Genome Research, Vol. 18, Issue 5 https://doi.org/10.1101/gr.074492.107	journal	February 2008
ABySS: A parallel assembler for short read sequence data Simpson, J. T.; Wong, K.; Jackman, S. D. Genome Research, Vol. 19, Issue 6 https://doi.org/10.1101/gr.089532.108	journal	February 2009
Assemblathon 1: A competitive assessment of de novo short read assembly methods Earl, D.; Bradnam, K.; St. John, J. Genome Research, Vol. 21, Issue 12 https://doi.org/10.1101/gr.126599.111	journal	September 2011
Efficient de novo assembly of large genomes using compressed data structures Simpson, J. T.; Durbin, R. Genome Research, Vol. 22, Issue 3 https://doi.org/10.1101/gr.126953.111	journal	December 2011
GAGE: A critical evaluation of genome assemblies and assembly algorithms Salzberg, S. L.; Phillippy, A. M.; Zimin, A. Genome Research, Vol. 22, Issue 3 https://doi.org/10.1101/gr.131383.111	journal	January 2012
Prevention, diagnosis and treatment of high-throughput sequencing data pathologies Zhou, Xiaofan; Rokas, Antonis Molecular Ecology, Vol. 23, Issue 7 https://doi.org/10.1111/mec.12680	journal	March 2014
Comparative genomics reveals insights into avian genome evolution and adaptation Zhang, G.; Li, C.; Li, Q. Science, Vol. 346, Issue 6215 https://doi.org/10.1126/science.1251385	journal	December 2014
The Genome Sequence of Drosophila melanogaster Adams, M. D. Science, Vol. 287, Issue 5461 https://doi.org/10.1126/science.287.5461.2185	journal	March 2000
Creating a Buzz About Insect Genomes Robinson, G. E.; Hackett, K. J.; Purcell-Miramontes, M. Science, Vol. 331, Issue 6023 https://doi.org/10.1126/science.331.6023.1386	journal	March 2011
The Theory and Practice of Genome Sequence Assembly Simpson, Jared T.; Pop, Mihai Annual Review of Genomics and Human Genetics, Vol. 16, Issue 1 https://doi.org/10.1146/annurev-genom-090314-050032	journal	August 2015
Assessment of de novoassemblers for draft genomes: a case study with fungal genomes Abbas, Mostafa M.; Malluhi, Qutaibah M.; Balakrishnan, Ponnuraman BMC Genomics, Vol. 15, Issue S9 https://doi.org/10.1186/1471-2164-15-s9-s10	journal	December 2014
Using cascading Bloom filters to improve the memory usage for de Brujin graphs Salikhov, Kamil; Sacomoto, Gustavo; Kucherov, Gregory Algorithms for Molecular Biology, Vol. 9, Issue 1 https://doi.org/10.1186/1748-7188-9-2	journal	January 2014
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species Bradnam, Keith R.; Fass, Joseph N.; Alexandrov, Anton GigaScience, Vol. 2, Issue 1 https://doi.org/10.1186/2047-217x-2-10	journal	July 2013
REAPR: a universal tool for genome assembly evaluation Hunt, Martin; Kikuchi, Taisei; Sanders, Mandy Genome Biology, Vol. 14, Issue 5 https://doi.org/10.1186/gb-2013-14-5-r47	journal	January 2013
Characterizing and measuring bias in sequence data Ross, Michael G.; Russ, Carsten; Costello, Maura Genome Biology, Vol. 14, Issue 5 https://doi.org/10.1186/gb-2013-14-5-r51	journal	January 2013
Automated ensemble assembly and validation of microbial genomes Koren, Sergey; Treangen, Todd J.; Hill, Christopher M. Springer Nature https://doi.org/10.13016/4pfi-yvf6	text	January 2014
Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies Denton, James F.; Lugo-Martinez, Jose; Tucker, Abraham E. PLoS Computational Biology, Vol. 10, Issue 12 https://doi.org/10.1371/journal.pcbi.1003998	journal	December 2014
Meraculous: De Novo Genome Assembly with Short Paired-End Reads Chapman, Jarrod A.; Ho, Isaac; Sunkara, Sirisha PLoS ONE, Vol. 6, Issue 8 https://doi.org/10.1371/journal.pone.0023501	journal	August 2011
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement Walker, Bruce J.; Abeel, Thomas; Shea, Terrance PLoS ONE, Vol. 9, Issue 11 https://doi.org/10.1371/journal.pone.0112963	journal	November 2014
Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi Ohm, Robin A.; Feau, Nicolas; Henrissat, Bernard PLoS Pathogens, Vol. 8, Issue 12 https://doi.org/10.1371/journal.ppat.1003037	journal	December 2012
Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis Goodwin, Stephen B.; M'Barek, Sarrah B.; Dhillon, Braham ETH Zurich https://doi.org/10.3929/ethz-b-000038874	text	January 2011
Informed and Automated k-Mer Size Selection for Genome Assembly Chikhi, Rayan; Medvedev, Paul arXiv https://doi.org/10.48550/arxiv.1304.5665	preprint	January 2013
Patterns of positive selection in seven ant genomes Roux, Julien; Privman, Eyal; Moretti, Sebastien arXiv https://doi.org/10.48550/arxiv.1311.4706	preprint	January 2013
Using Cascading Bloom Filters to Improve the Memory Usage for de Brujin Graphs Salikhov, Kamil; Sacomoto, Gustavo; Kucherov, Gregory Lecture Notes in Computer Science https://doi.org/10.1007/978-3-642-40453-5_28	book	January 2013
The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae Foury, Françoise; Roganti, Tiziana; Lecrenier, Nicolas FEBS Letters, Vol. 440, Issue 3 https://doi.org/10.1016/S0014-5793(98)01467-7	journal	December 1998
Genomics and the making of yeast biodiversity Hittinger, Chris Todd; Rokas, Antonis; Bai, Feng-Yan Current Opinion in Genetics & Development, Vol. 35 https://doi.org/10.1016/j.gde.2015.10.008	journal	December 2015
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana No authors listed Nature, Vol. 408, Issue 6814, p. 796-815 https://doi.org/10.1038/35048692	journal	December 2000
Overview of the yeast genome Mewes, H. W.; Albermann, K.; Bähr, M. Nature, Vol. 387, Issue S6632 https://doi.org/10.1038/387s007	journal	May 1997
Erratum: Overview of the yeast genome Mewes, H. W.; Albermann, K.; Bähr, M. Nature, Vol. 387, Issue 6634 https://doi.org/10.1038/42755	journal	June 1997
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing Berlin, Konstantin; Koren, Sergey; Chin, Chen-Shan Nature Biotechnology, Vol. 33, Issue 6 https://doi.org/10.1038/nbt.3238	journal	May 2015
Fueling the future with fungal genomics Grigoriev, Igor V.; Cullen, Daniel; Goodwin, Stephen B. Mycology, Vol. 2, Issue 3 https://doi.org/10.1080/21501203.2011.584577	journal	July 2011
Informed and automated k-mer size selection for genome assembly Chikhi, R.; Medvedev, P. Bioinformatics, Vol. 30, Issue 1 https://doi.org/10.1093/bioinformatics/btt310	journal	June 2013
Patterns of Positive Selection in Seven Ant Genomes Roux, Julien; Privman, Eyal; Moretti, Sébastien Molecular Biology and Evolution, Vol. 31, Issue 7 https://doi.org/10.1093/molbev/msu141	journal	April 2014
The Genome Sequence of Saccharomyces eubayanus and the Domestication of Lager-Brewing Yeasts Baker, EmilyClare; Wang, Bing; Bellora, Nicolas Molecular Biology and Evolution, Vol. 32, Issue 11 https://doi.org/10.1093/molbev/msv168	journal	August 2015
Error correction and assembly complexity of single molecule sequencing reads Lee, Hayan; Gurtowski, James; Yoo, Shinjae bioRxiv https://doi.org/10.1101/006395	posted_content	June 2014
Finished bacterial genomes from shotgun sequence data Ribeiro, F. J.; Przybylski, D.; Yin, S. Genome Research, Vol. 22, Issue 11 https://doi.org/10.1101/gr.141515.112	journal	July 2012
Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads Kajitani, Rei; Toshimoto, Kouta; Noguchi, Hideki Genome Research, Vol. 24, Issue 8 https://doi.org/10.1101/gr.170720.113	journal	April 2014
Field guide to next-generation DNA sequencers: FIELD GUIDE TO NEXT-GEN SEQUENCERS Glenn, Travis C. Molecular Ecology Resources, Vol. 11, Issue 5 https://doi.org/10.1111/j.1755-0998.2011.03024.x	journal	May 2011
A Whole-Genome Assembly of Drosophila Myers, E. W. Science, Vol. 287, Issue 5461 https://doi.org/10.1126/science.287.5461.2196	journal	March 2000
Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee Chang, Jia-Ming; Di Tommaso, Paolo; Taly, Jean-Francois BMC Bioinformatics, Vol. 13, Issue Suppl 4 https://doi.org/10.1186/1471-2105-13-S4-S1	journal	January 2012
Exploiting sparseness in de novo genome assembly Ye, Chengxi; Ma, Zhanshan Sam; Cannon, Charles H. BMC Bioinformatics, Vol. 13, Issue S6 https://doi.org/10.1186/1471-2105-13-S6-S1	journal	April 2012
Automated ensemble assembly and validation of microbial genomes Koren, Sergey; Treangen, Todd J.; Hill, Christopher M. BMC Bioinformatics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2105-15-126	journal	May 2014
Assessment of de novoassemblers for draft genomes: a case study with fungal genomes Abbas, Mostafa M.; Malluhi, Qutaibah M.; Balakrishnan, Ponnuraman BMC Genomics, Vol. 15, Issue S9 https://doi.org/10.1186/1471-2164-15-S9-S10	journal	December 2014
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler Luo, Ruibang; Liu, Binghang; Xie, Yinlong GigaScience, Vol. 1, Issue 1 https://doi.org/10.1186/2047-217X-1-18	journal	December 2012
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species Bradnam, Keith R.; Fass, Joseph N.; Alexandrov, Anton GigaScience, Vol. 2, Issue 1 https://doi.org/10.1186/2047-217X-2-10	journal	July 2013
Reducing assembly complexity of microbial genomes with single-molecule sequencing Koren, Sergey; Harhay, Gregory P.; Smith, Timothy PL Genome Biology, Vol. 14, Issue 9 https://doi.org/10.1186/gb-2013-14-9-r101	journal	January 2013
Metassembler: merging and optimizing de novo genome assemblies Wences, Alejandro Hernandez; Schatz, Michael C. Genome Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s13059-015-0764-4	journal	September 2015
Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis Goodwin, Stephen B.; Ben M'Barek, Sarrah; Dhillon, Braham PLoS Genetics, Vol. 7, Issue 6 https://doi.org/10.1371/journal.pgen.1002070	journal	June 2011
Evaluation of Methods for De Novo Genome Assembly from High-Throughput Sequencing Reads Reveals Dependencies That Affect the Quality of the Results Haiminen, Niina; Kuhn, David N.; Parida, Laxmi PLoS ONE, Vol. 6, Issue 9 https://doi.org/10.1371/journal.pone.0024182	journal	September 2011
Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research McIlwain, Sean J.; Peris, David; Sardi, Maria G3: Genes\|Genomes\|Genetics, Vol. 6, Issue 6 https://doi.org/10.1534/g3.116.029389	journal	April 2016
Metassembler: merging and optimizing de novo genome assemblies Wences, Alejandro; Schatz, Michael Figshare https://doi.org/10.6084/m9.figshare.c.3642413	collection	January 2015

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