COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly

Liu, Binghang, Yuan, Jianying, Yiu, Siu-Ming, Li, Zhenyu, Xie, Yinlong, Chen, Yanxiang, Shi, Yujian, Zhang, Hao +3 more·2012·Bioinformatics

Cited by (138)

Items 101–138 of 138

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    Candela García‐Gómez, Lidia Yebra, Dolores Cortés, Antonio Sánchez, Aitor Alonso, Nerea Valcárcel‐Pérez, Francisco Gómez-Jakobsen, Inma Herrera, Carolina Johnstone, Jesús M. Mercado · 2020 · FEMS Microbiology Ecology
  3. Inoculum effect of arbuscular mycorrhizal fungi on soybeans grown in long-term bare-fallowed field with low phosphate availability
    Masaki Hayashi, Rieko Niwa, Yasufumi Urashima, 有子 須賀, Shusei Sato, Hideki Hirakawa, Shigenobu Yoshida, Tatsuhiro Ezawa, 敏彦 唐澤 · 2018 · Soil Science & Plant Nutrition
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  6. Optimizing Information in Next-Generation-Sequencing (NGS) Reads for Improving De Novo Genome Assembly
    Tsunglin Liu, Cheng-Hung Tsai, Wen-Bin Lee, Jung-Hsien Chiang · 2013 · PLoS ONE
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    Emily E. Puckett, Sean M. Murphy, Gideon S. Bradburd · 2021 · Ecology and Evolution
  8. Metabarcoding reveals seasonal and spatial patterns of arthropod community assemblages in two contrasting habitats: Desert and oasis of the Baja California Peninsula, Mexico
    Anastasia Klimova, Ricardo Rodríguez‐Estrella, Guanliang Meng, Jesús Neftalí Gutiérrez‐Rivera, María Luisa Jimenez‐Jimenez, Shanlin Liu · 2023 · Diversity and Distributions
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    Steven D. Quistad, Yan Wei Lim, Genivaldo Gueiros Z. Silva, Craig E. Nelson, Andreas Florian Haas, Linda Wegley Kelly, Robert Alan Edwards, Forest L. Rohwer · 2016 · Proceedings of the Royal Society B Biological Sciences
  10. MERIT reveals the impact of genomic context on sequencing error rate in ultra-deep applications
    Mohammad Hadigol, Hossein Khiabanian · 2018 · BMC Bioinformatics
  11. From Short Reads to Chromosome-Scale Genome Assemblies
    Kyle Fletcher, Richard W. Michelmore · 2018 · Methods in molecular biology
  12. De novo assembly of transcriptome from next‐generation sequencing data
    Xuan Li, Yimeng Kong, Qiongyi Zhao, Yuanyuan Li, Pei Hao · 2016 · Quantitative Biology
  13. Determinants of genetic diversity in Neotropical salamanders (Plethodontidae: Bolitoglossini)
    María Guadalupe Segovia‐Ramírez, Obed Ramírez‐Sánchez, Louis Paul Decena-Segarra, Hairo Rios‐Carlos, Sean M. Rovito · 2023 · Ecology and Evolution
  14. Genomic sequencing of Troides aeacus nucleopolyhedrovirus (TraeNPV) from golden birdwing larvae (Troides aeacus formosanus) to reveal defective Autographa californica NPV genomic features
    Yu‐Feng Huang, Tzu-Han Chen, Zih-Ting Chang, Tai-Chuan Wang, Se Jin Lee, Jong Cheol Kim, Jae Su Kim, Kuo‐Ping Chiu, Yu‐Shin Nai · 2019 · BMC Genomics
  15. Analysis of Quasispecies of Avain Leukosis Virus Subgroup J Using Sanger and High-throughput Sequencing
    Fanfeng Meng, Xuan Dong, Tao Hu, Yingnan Liu, Yingjie Zhao, Yanyan Lv, Shuang Chang, Peng Zhao, Zhizhong Cui · 2016 · Virology Journal
  16. Using full-length metabarcoding and DNA barcoding to infer community assembly for speciose taxonomic groups: a case study
    Meng‐di Hao, Qian Jin, Guanliang Meng, Cai‐qing Yang, Shenzhou Yang, Zhiyong Shi, Min Tang, Shanlin Liu, Yinan Li, Jing Li et al. · 2020 · Evolutionary Ecology
  17. Magnus representation of genome sequences
    Chengyuan Wu, Shiquan Ren, Jie Wu, Kelin Xia · 2019 · Journal of Theoretical Biology
  18. BigFiRSt: A Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing Data
    Jin-Xiang Chen, Fuyi Li, Miao Wang, Jun‐Long Li, Tatiana T. Marquez‐Lago, André Leier, Jerico Revote, Shuqin Li, Quanzhong Liu, Jiangning Song · 2022 · Frontiers in Big Data
  19. Determination of Nucleopolyhedrovirus’ Taxonomic Position
    Yu‐Shin Nai, Yu‐Feng Huang, Tzu-Han Chen, Kuo‐Ping Chiu, Chung‐Hsiung Wang · 2017 · InTech eBooks
  20. Tracking an Introduced Arbuscular Mycorrhizal Fungus in Allium fistulosum in a Field Condition With or Without Controlling Indigenous Fungi by Soil Fumigation As Well as Evaluation on Plant Phosphorus and Growth
    Takumi Sato, Rieko Niwa, Tatsuhiro Ezawa, Shusei Sato, Hideki Hirakawa, Shigenobu Yoshida, Weiguo Cheng, Keitaro Tawaraya · 2021 · Journal of soil science and plant nutrition
  21. Rising Strengths Hong Kong SAR in Bioinformatics
    Chiranjib Chakraborty, C. George Priya Doss, Hailong Zhu, Govindasamy Agoramoorthy · 2016 · Interdisciplinary Sciences Computational Life Sciences
  22. Sequencing Ancestor Diploid Genomes for Enhanced Genome Understanding and Peanut Improvement
    Spurthi N. Nayak, Manish Kumar Pandey, Scott A. Jackson, Xuanqiang Liang, Rajeev Kumar Varshney · 2017 · Compendium of plant genomes
  23. CAREx: context-aware read extension of paired-end sequencing data
    Felix Kallenborn, Bertil Schmidt · 2024 · BMC Bioinformatics
  24. DUDE-Seq: Fast, flexible, and robust denoising of nucleotide sequences
    Byunghan Lee, Taesup Moon, Sungroh Yoon, Tsachy Weissman · 2015 · arXiv (Cornell University)
  25. IMperm: a fast and comprehensive IMmune Paired-End Reads Merger for sequencing data
    Wei Zhang, Jia Ju, Yong Zhou, Teng Xiong, Mengyao Wang, Chaohui Li, Shixin Lu, Zefeng Lu, Liya Lin, Xiao Liu et al. · 2023 · Briefings in Bioinformatics
  26. Profiling the Gut Microbiome: Practice and Potential
    Toral Manvar, Vijay Lakhujani · 2018 · Elsevier eBooks
  27. Bacterial biogeography of the rare Charitable Research Reserve
    Brent J. Seuradge · 2015 · UWSpace (University of Waterloo)
  28. Planck Institute for Evolutionary Biology Research Group Leader: Honorarprofessor Dr.
    Bernhard Haubold, Phylogenetic Marker Analysis · 2014
  29. MeFiT: Merging and Filtering Tool for Illumina Paired-End Reads for 16S rRNA Amplicon Sequencing
    Hardik I. Parikh, Vishal N. Kopardé, Bradley, Steven P., Gregory A. Buck, Nihar U. Sheth · 2015 · arXiv (Cornell University)
  30. orthoCapture: Facilitating Gene Capture Probe Design for Non-Model Species
    M. Elise Lauterbur · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  31. Transcriptome-based identification of small RNA in plants: The need for robust prediction algorithms
    Sayak Ganguli, Pankaj Kumar Singh, Amita Pal · 2020 · Elsevier eBooks
  32. Overview of ApproachesFrom Whole‐Community Shotgun Sequencing to Single‐Cell Genomics
    Gregory J. Dick · 2018
  33. Profiling the Gut Microbiome: Practice and Potential
    Muhammed Erkan Karabekmez, Kadir Volkan Sak · 2024 · Elsevier eBooks
  34. Human Leukocyte Antigen Genotypes Affect Hepatitis B Virus Mutations Associated With Hepatocellular Carcinoma
    Masaya Sugiyama, Nao Nishida, Seik‐Soon Khor, Tadasu Shin‐I, Keisuke Hino, Masao Honda, Shuichi Kaneko, Hiroshi Yatsuhashi, Kazuhiko Koike, Masayuki Kurosaki et al. · 2025 · Hepatology Research
  35. Additional file 1 of CAREx: context-aware read extension of paired-end sequencing data
    Felix Kallenborn, Schmidt Bertil · 2024 · Figshare
  36. Microbial community structures are associated with medicinal bioactive compound accumulation in Drynaria roosii Nakaike across rock and tree habitats
    Bo Wang, Fuli-Gong, Chunjiang-Huang, Jingzhong-Chen, Pengjie-He, Hongyu Chen, Wenyan-Cui, Qingwen-Sun · 2026 · Rhizosphere
  37. Evolution des génomes polyploïdes et innovations fonctionnelles : contexte phylogénétique et origine du DMSP chez les spartines
    Hélène Rousseau · 2017
  38. A bacterial pangenome association study identifies a role for polyamine metabolism and alkaline tolerance in middle ear infections
    Jocelyn A. Hammond, Rachel L. Ehrlich, Ariel Gonzalez, Begoña Euba, Kevin M. Raible, Jill M. Lawrence, Ari B. Gordon, Evangeline Williams, Mary C. Marino, Jason Limbo et al. · 2026 · PLoS Pathogens