The Phusion Assembler

Mullikin, James C., Ning, Zemin·2003·Genome Research
DOI 10.1101/gr.731003

Cited by (222)

Items 101–200 of 222

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  5. Whole genome shotgun sequencing guided by bioinformatics pipelines—an optimized approach for an established technique
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  6. Genomic resources for the endangered Hawaiian honeycreepers
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  8. De novo assembly methods for next generation sequencing data
    Yiming He, Zhen Zhang, Xiaoqing Peng, Fang‐Xiang Wu, Jianxin Wang · 2013 · Tsinghua Science & Technology
  9. Sequencing smart: De novo sequencing and assembly approaches for a non-model mammal
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  10. A Tool for Analyzing Mate Pairs in Assemblies (TAMPA)
    Ian M. Dew, Brian P. Walenz, Granger Sutton · 2005 · Journal of Computational Biology
  11. Next-Generation Sequencing (NGS) Tools and Impact in Plant Breeding
    Vinay Kumar Singh, Anil Kumar Singh, Sakshi Singh, Brahma Deo Singh · 2015 · Springer eBooks
  12. A deep dive into genome assemblies of non-vertebrate animals
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  13. De novo repeat classification and fragment assembly
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  14. Building and Improving Reference Genome Assemblies
    Karyn Meltz Steinberg, Valérie Schneider, Can Alkan, Michael J. Montague, Wesley C. Warren, Deanna M. Church, Richard K. Wilson · 2017 · Proceedings of the IEEE
  15. Computational Biology Methods and Their Application to the Comparative Genomics of Endocellular Symbiotic Bacteria of Insects
    Jennifer M. Commins, Christina Toft, Mario A. Fares · 2009 · Biological Procedures Online
  16. Revamp a model—status and prospects of the Dictyostelium genome project
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  17. Statistical Significance of Optical Map Alignments
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  18. Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences
    Song Gao, Niranjan Nagarajan, Wing-Kin Ken Sung · 2011 · Lecture notes in computer science
  19. GAM: Genomic Assemblies Merger: A Graph Based Method to Integrate Different Assemblies
    Alberto Casagrande, Cristian Del Fabbro, Simone Scalabrin, Alberto Policriti · 2009 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
  20. Targeted annotation of immunoglobulin light chain (IgL) genes in zebrafish from BAC clones reveals kappa-like recombining/deleting elements within IgL constant regions
    Anastasia M. Zimmerman, Krzysztof E. Romanowski, Benjamin J. Maddox · 2010 · Fish & Shellfish Immunology
  21. Cloning of the cDNA for murine von Willebrand factor and identification of orthologous genes reveals the extent of conservation among diverse species
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  22. Gap statistics for whole genome shotgun DNA sequencing projects
    Michael C. Wendl, Shiaw‐Pyng Yang · 2004 · Bioinformatics
  23. Genome Sequencing and Assembly
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  24. Genome Sequencing Technology and Algorithms
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  25. A rapid method for detection of putative RNAi target genes in genomic data
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  26. Genome Sequence Databases (Overview): Sequencing and Assembly
    Alla L Lapidus · 2009 · University of North Texas Digital Library (University of North Texas)
  27. IDBA-MTP: A Hybrid MetaTranscriptomic Assembler Based on Protein Information
    Henry C. M. Leung, Siu‐Ming Yiu, Francis Y. L. Chin · 2014 · Lecture notes in computer science
  28. Chaining Algorithms for Alignment of Draft Sequence
    Mukund Sundararajan, Michael Brudno, Kerrin S. Small, Arend Sidow, Serafim Batzoglou · 2004 · Lecture notes in computer science
  29. Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly
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  31. Development of Novel Microsatellite Markers for the BBCC Oryza Genome (Poaceae) Using High-Throughput Sequencing Technology
    Caihong Wang, Xiaojiao Liu, Suo-tang PENG, Qun Jie Xu, Xiaoping Yuan, Yue Feng, Hanyong Yu, Yiping Wang, Xinghua Wei · 2014 · PLoS ONE
  32. The complexity of Rhipicephalus (Boophilus) microplus genome characterised through detailed analysis of two BAC clones
    Paula Moolhuijzen, Ala E. Tabor, Jess A. T. Morgan, Manuel Rodriguez-Valle, Daniel G. Peterson, Scot E. Dowd, Felix David Guerrero, M. Bellgard, R. Appels · 2011 · BMC Research Notes
  33. Algorithmic challenges in mammalian whole‐genome assembly
    Serafim Batzoglou · 2005 · Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics
  34. Management and Visualization of Whole Genome Shotgun Assemblies Using SAM
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  35. Building Fragment Assembly String Graphs
    Eugene Wimberly Myers · 2005
  36. Genome Sequence Databases: Sequencing and Assembly
    Alla L Lapidus · 2009 · Elsevier eBooks
  37. An improved maximum likelihood formulation for accurate genome assembly
    Aditya Padmanabhan Varma, Abhiram Ranade, Srinivas Aluru · 2011 · IEEE International Conference on Computational Advances in Bio and Medical Sciences
  38. Genomes of the willow-galling sawflies Euura lappo and Eupontania aestiva (Hymenoptera: Tenthredinidae): a resource for research on ecological speciation, adaptation, and gall induction
    Craig Michell, Saskia Wutke, Manuel Aranda, Tommi Nyman · 2021 · G3 Genes Genomes Genetics
  39. Assembling genomes on large-scale parallel computers
    Ananth Kalyanaraman, Scott Emrich, Patrick S. Schnable, S. Aluru · 2006 · IEEE International Parallel and Distributed Processing Symposium (IPDPS)
  40. Genome assembly and annotation
    Pallavi Mishra, Ranjeet Maurya, Himanshu Avashthi, Shikha Mittal, Muktesh Chandra, Pramod Wasudeo Ramteke · 2021 · Elsevier eBooks
  41. Construction and Application of Genomic DNA Libraries
    Hye Ran Kim, Tae‐Jin Yang, David A. Kudrna, Rod A. Wing · 2004
  42. SparseAssembler: de novo Assembly with the Sparse de Bruijn Graph
    Chengxi Ye, Zhanshan Sam Ma, Charles H. Cannon, Mihai Pop, Douglas W. Yu · 2011 · arXiv (Cornell University)
  43. Plant genome sequencing
    Delphine Fleury, Ute Baumann, Peter Langridge · 2011 · Elsevier eBooks
  44. Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps
    Michael Roberts, Aleksey V. Zimin, Wayne B. Hayes, Brian R. Hunt, Cevat Üstün, James Robert White, Paul Havlak, James A. Yorke · 2008 · PLoS ONE
  45. Artifacts of the 1.9x Feline Genome Assembly Derived from the Feline-Specific Satellite Sequence
    Joan U. Pontius, Stephen J. O’Brien · 2009 · Journal of Heredity
  46. A transcriptomics approach to understanding polymorphic and transcript level differences linked to isoquinoline alkaloid production in triploid varieties of narcissus pseudonarcissus
    Jane A. Pulman · 2015 · University of Liverpool
  47. Etat actuel du séquençage et de la connaissance du génome des espèces animales
    Alain Vignal A · 2011 · INRAE Productions Animales
  48. A Combined Approach for de novo DNA Sequence Assembly of Very Short Reads
    Wisnu Ananta Kusuma, Takashi Ishida, Yutaka Akiyama · 2011 · IPSJ Transactions on Bioinformatics
  49. Back to Bermuda: how is science best served?
    Deanna M. Church, LaDeana Hillier · 2009 · Genome biology
  50. De novo assembly of 20 chickens reveals the undetectable phenomenon for thousands of core genes on sub-telomeric regions
    Ming Li, Congjiao Sun, Naiyi Xu, Peipei Bian, Xiaomeng Tian, Xihong Wang, Yuzhe Wang, Xinzheng Jia, Rasmus Heller, Mingshan Wang et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  51. Chapter 11 Genome Sequencing and Assembly
    Annette McGrath · 2007 · Perspectives in bioanalysis
  52. A survey of genome sequence assembly techniques and algorithms using high-performance computing
    Munib Ahmed, Ishfaq Ahmad D, Mohammad Saad Ahmad · 2014 · The Journal of Supercomputing
  53. Assessing the Quality of Finished Genomic Sequence
    Jeremy Schmutz, Jeremy Wheeler, Jane Grimwood, Mark C. Dickson, R Myers · 2003 · Cold Spring Harbor Symposia on Quantitative Biology
  54. benchNGS : An approach to benchmark short reads alignment tools
    Farzana Rahman, Mehedi Hassan, Alona Kryshchenko, Inna L Dubchak, Nickolai N. Alexandrov, Tatiana V. Tatarinova · 2015 · bioRxiv (Cold Spring Harbor Laboratory)
  55. Phylogenomics analyses of all species of Swordtails (Genus Xiphophorus ) highlights hybridization precedes speciation
    Kang Du, Yuan Lü, Mateo García-Olazábal, Ronald B. Walter, Wesley C. Warren, Tristram O. Dodge, Molly E. Schumer, Hyun Park, Axel Meyer, Manfred Schartl · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  56. Draft Genome Sequences of Vibrio alginolyticus Strain S6-61 and Vibrio diabolicus Strain S7-71, Isolated from Corals in the Andaman Sea
    Sushanta Deb, Jhasketan Badhai, Subrata K. Das · 2020 · Microbiology Resource Announcements
  57. Silkworm genomics
    Manjunatha Hosaholalu Boregowda · 2020 · Elsevier eBooks
  58. Accurate assembly of full-length consensus for viral quasispecies
    Tian Jia, Ziyu Gao, Minghao Li, Ergude Bao, Jin Zhao · 2025 · BMC Bioinformatics
  59. Sequencing Strategies for Parasite Genomes
    Daniella Castanheira Bartholomeu, Najib M. El-Sayed · 2004 · Humana Press eBooks
  60. Next-Generation Sequencing and Assembly of Plant Genomes
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  61. Sequence Assembly
    Xiaoqiu Huang · 2016 · Methods in molecular biology
  62. Genome Sequence Databases: Sequencing and Assembly☆
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  63. Whole Genome Sequencing: Methodology and Progress in Cereals
    Yeisoo Yu, Rod A. Wing · 2006 · Kluwer Academic Publishers eBooks
  64. Expressed Sequence Tags: Clustering and Applications
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  65. A De Novo Metagenomic Assembly Program for Shotgun DNA Reads
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  66. The human genome project: software challenges and future directions
    N. Stojanovic · 2005 · IEEE/ACS International Conference on Computer Systems and Applications (AICCSA)
  67. Recent Advances in Gene and Genome Assembly: Challenges and Implications
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  68. Learning pair-wise gene functional similarity by multiplex gene expression maps
    Li An, Haibin Ling, Zoran Obradovic A, Desmond Smith, Vasileios Megalooikonomou · 2012 · BMC Bioinformatics
  69. MULKSG: MULtiple K Simultaneous Graph Assembly
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  70. Sequencing the Human Genome: A Historical Perspective on Challenges for Systems Integration
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  71. Bioinformatics Support for Genome‐Sequencing Projects
    Knut Reinert, Daniel H. Huson · 2007
  72. Solving repeat problems in shotgun sequencing
    Peter Arner · 2006 · Figshare
  73. Algorithms for Large-Scale Clustering and Assembly of Biological Sequence Data
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  74. A De Novo Metagenomic Assembly Program for Shotgun DNA Reads
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  75. An Algorithm for the Automated Verification of DNA Supercontig Assemblies
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  76. Strategy and Tactics for Genome Sequencing
    Michael C. Zody, Chad Nusbaum · 2008
  77. Rodent malaria parasites : genome organization & comparative genomics
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  78. Genome signals and assembly
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  79. High-performance Computing Methods for Computational Genomics
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  80. Errors in sequence assembly and corrections
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  81. A New Data Clustering Algorithm for Parallel Whole-Genome Shotgun Sequence Assembly
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  82. Large-Scale DNA Sequence Assembly by Using Computing Grid
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  83. A de novo assembly method for metagenomic DNA reads with mate pairs
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  84. benchNGS : An approach to benchmark short reads alignment tools
    Farzana Rahman, Mehedi Hassan, Alona Kryshchenko, Inna L Dubchak, Tatiana V. Tatarinova, Nickolai N. Alexandrov · 2015
  85. Whole genome assembly and gap closure of the toxic bloom-forming cyanobacterium Anabaena sp. strain 90
    Hao Wang · 2008 · Työväentutkimus Vuosikirja
  86. Improving Sequence Assembly of the Rat Genome Using Reliable Overlaps and Extended Reads
    Wayne B. Hayes, Brian R. Hunt, Michael Roberts, James A. Yorke, Aleksey V. Zimin, Paul Havlak · 2005
  87. Heterogeneous multi-core systems for bioinformatics
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  88. Insights into the origins and evolution of mutualistic insect-bacterial symbioses
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  89. Computational identification and analysis of evolutionary breakpoint regions in amniote genomes
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  90. graphsAlgorithms for de novo short read assembly using de Bruijn
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  91. Characterization of de novo assemblies of quasispecies from next- generation sequencing via complex network modeling
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  94. DNA Sequencing for the Detection of Human Genome Variation
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  95. DNA Sequencing for the Detection of Human Genome Variation and Polymorphism
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  96. Algorithms for structural variation discovery using multiple sequence signatures
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  97. Repetitive DNA sequence assembly
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  98. Evaluation of genome scaffolding tools using pooled clone sequencing
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  99. Comparative Genomics
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