in silico Whole Genome Sequencer & Analyzer (iWGS): a computational pipeline to guide the design and analysis of de novo genome sequencing studies
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Antonis Rokas | David Peris | Xiaofan Zhou | Chris Todd Hittinger | A. Rokas | Jacek Kominek | C. Kurtzman | C. T. Hittinger | D. Peris | Xiaofan Zhou | Jacek Kominek | Cletus P Kurtzman
[1] M. Schatz,et al. Algorithms Gage: a Critical Evaluation of Genome Assemblies and Assembly Material Supplemental , 2008 .
[2] Alexey A. Gurevich,et al. QUAST: quality assessment tool for genome assemblies , 2013, Bioinform..
[3] Sergey Koren,et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.
[4] M. Schatz,et al. Phased diploid genome assembly with single-molecule real-time sequencing , 2016, Nature Methods.
[5] S. Carroll,et al. Genome-scale approaches to resolving incongruence in molecular phylogenies , 2003, Nature.
[6] Inanç Birol,et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species , 2013, GigaScience.
[7] C. Nusbaum,et al. Finished bacterial genomes from shotgun sequence data , 2012, Genome research.
[8] Daniel Mapleson,et al. RAMPART: a workflow management system for de novo genome assembly , 2015, Bioinform..
[9] Sergey Koren,et al. Automated ensemble assembly and validation of microbial genomes , 2014, BMC Bioinformatics.
[10] Jian Wang,et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.
[11] Isaac Y. Ho,et al. Meraculous: De Novo Genome Assembly with Short Paired-End Reads , 2011, PloS one.
[12] Zhen Yue,et al. pIRS: Profile-based Illumina pair-end reads simulator , 2012, Bioinform..
[13] Joshua M. Stuart,et al. Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. , 2009, The Journal of heredity.
[14] Stephen M. Mount,et al. The genome sequence of Drosophila melanogaster. , 2000, Science.
[15] Christina A. Cuomo,et al. Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement , 2014, PloS one.
[16] J. Rayner,et al. Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts , 2014, Nature Communications.
[17] Antonis Rokas,et al. Inferring ancient divergences requires genes with strong phylogenetic signals , 2013, Nature.
[18] M. Berriman,et al. REAPR: a universal tool for genome assembly evaluation , 2013, Genome Biology.
[19] The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.
[20] Cédric Notredame,et al. Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee , 2012, BMC Bioinformatics.
[21] E. Birney,et al. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.
[22] Gregory Kucherov,et al. Using cascading Bloom filters to improve the memory usage for de Brujin graphs , 2013, Algorithms for Molecular Biology.
[23] Miriam L. Land,et al. Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences , 2014, Bioinform..
[24] Eugene W. Myers,et al. A whole-genome assembly of Drosophila. , 2000, Science.
[25] James G. Baldwin-Brown,et al. Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage , 2016, bioRxiv.
[26] Paul Medvedev,et al. Informed and automated k-mer size selection for genome assembly , 2013, Bioinform..
[27] Steven J. M. Jones,et al. Abyss: a Parallel Assembler for Short Read Sequence Data Material Supplemental Open Access , 2022 .
[28] A. Gnirke,et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data , 2010, Proceedings of the National Academy of Sciences.
[29] Nikos Kyrpides,et al. The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification , 2014, Nucleic Acids Res..
[30] Jonathan E. Allen,et al. Genome sequence of the human malaria parasite Plasmodium falciparum , 2002, Nature.
[31] Leping Li,et al. ART: a next-generation sequencing read simulator , 2012, Bioinform..
[32] M. Schatz,et al. Phased diploid genome assembly with single-molecule real-time sequencing , 2016, Nature Methods.
[33] B. Purnelle,et al. The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae , 1998, FEBS letters.
[34] Josephine T. Daub,et al. Patterns of Positive Selection in Seven Ant Genomes , 2013, Molecular biology and evolution.
[35] N. Loman,et al. A complete bacterial genome assembled de novo using only nanopore sequencing data , 2015, Nature Methods.
[36] D. Hibbett,et al. Fueling the future with fungal genomics , 2011 .
[37] Steven Salzberg,et al. GAGE-B: an evaluation of genome assemblers for bacterial organisms , 2013, Bioinform..
[38] T. Glenn. Field guide to next‐generation DNA sequencers , 2011, Molecular ecology resources.
[39] Nuno A. Fonseca,et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. , 2011, Genome research.
[40] Susan J. Brown,et al. Creating a buzz about insect genomes. , 2011, Science.
[41] M. Pop,et al. The Theory and Practice of Genome Sequence Assembly. , 2015, Annual review of genomics and human genetics.
[42] Timothy P. L. Smith,et al. Reducing assembly complexity of microbial genomes with single-molecule sequencing , 2013, Genome Biology.
[43] Andreas R. Pfenning,et al. Comparative genomics reveals insights into avian genome evolution and adaptation , 2014, Science.
[44] Shoshana Marcus,et al. Error correction and assembly complexity of single molecule sequencing reads , 2014, bioRxiv.
[45] A. Friedrich,et al. Mitochondrial genome evolution in yeasts: an all-encompassing view. , 2015, FEMS yeast research.
[46] S. Koren,et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.
[47] S. Oliver,et al. Erratum: Overview of the yeast genome , 1997, Nature.
[48] M. Schatz,et al. Metassembler: merging and optimizing de novo genome assemblies , 2015, Genome Biology.
[49] Michael Roberts,et al. The MaSuRCA genome assembler , 2013, Bioinform..
[50] Mihai Pop,et al. Exploiting sparseness in de novo genome assembly , 2012, BMC Bioinformatics.
[51] H. Mewes,et al. Overview of the yeast genome. , 1997, Nature.
[52] Jose Lugo-Martinez,et al. Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies , 2014, PLoS Comput. Biol..
[53] S. Koren,et al. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. , 2015, Current opinion in microbiology.
[54] B. Wang,et al. The Genome Sequence of Saccharomyces eubayanus and the Domestication of Lager-Brewing Yeasts , 2015, Molecular biology and evolution.
[55] I. Rigoutsos,et al. Evaluation of Methods for De Novo Genome Assembly from High-Throughput Sequencing Reads Reveals Dependencies That Affect the Quality of the Results , 2011, PloS one.
[56] M. Pop,et al. Sequence assembly demystified , 2013, Nature Reviews Genetics.
[57] Sudhir Kumar,et al. Mutation rates in mammalian genomes , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[58] T. Jeffries,et al. Genomics and the making of yeast biodiversity. , 2015, Current opinion in genetics & development.
[59] L. Solieri,et al. Mitochondrial inheritance in budding yeasts: towards an integrated understanding. , 2010, Trends in microbiology.
[60] Sergey I. Nikolenko,et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..
[61] R. Durbin,et al. Efficient de novo assembly of large genomes using compressed data structures. , 2012, Genome research.
[62] Paramvir S. Dehal,et al. Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis , 2011, PLoS genetics.
[63] Chengxi Ye,et al. DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies , 2014, Scientific Reports.
[64] Antonis Rokas,et al. Harnessing genomics for evolutionary insights. , 2009, Trends in ecology & evolution.
[65] A. Salamov,et al. Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi , 2012, PLoS pathogens.
[66] D. Posada,et al. Simulation of Genome-Wide Evolution under Heterogeneous Substitution Models and Complex Multispecies Coalescent Histories , 2014, Molecular biology and evolution.
[67] Aaron A. Klammer,et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data , 2013, Nature Methods.
[68] J. Landolin,et al. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing , 2014, Nature Biotechnology.
[69] Kiyoshi Asai,et al. PBSIM: PacBio reads simulator - toward accurate genome assembly , 2013, Bioinform..
[70] Ponnuraman Balakrishnan,et al. Assessment of de novo assemblers for draft genomes: a case study with fungal genomes , 2014, BMC Genomics.
[71] Antonis Rokas,et al. Prevention, diagnosis and treatment of high‐throughput sequencing data pathologies , 2014, Molecular ecology.
[72] Irene M Ong,et al. Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research , 2016, G3: Genes, Genomes, Genetics.
[73] C. Nusbaum,et al. Comprehensive variation discovery in single human genomes , 2014, Nature Genetics.
[74] N. Lennon,et al. Characterizing and measuring bias in sequence data , 2013, Genome Biology.
[75] Tetsuya Hayashi,et al. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads , 2014, Genome research.