Efficient de novo assembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit
暂无分享,去创建一个
Adam M. Phillippy | David Haussler | Joel Armstrong | Benedict Paten | Tobias Marschall | Mark Akeson | Colleen M. Bosworth | Richard E. Green | Justin M. Zook | Fritz J. Sedlazeck | Kishwar Shafin | Trevor Pesout | Miten Jain | Sergey Koren | Mitchell R. Vollger | Karen H. Miga | Marina Haukness | Kelvin J. Liu | Evan E. Eichler | Sofie R. Salama | Ryan Lorig-Roach | Hugh E. Olsen | Kristof Tigyi | Nicholas W. Maurer | Simon C Mayes | Vania Costa | Kelvin J. Liu | Duncan Kilburn | Melanie Sorensen | Katy M. Munson | Paolo Carnevali | D. Haussler | P. Carnevali | E. Eichler | S. Koren | A. Phillippy | J. Zook | B. Paten | R. Green | F. Sedlazeck | T. Marschall | S. Salama | J. Armstrong | Miten Jain | M. Akeson | Kristof Tigyi | D. Kilburn | Kishwar Shafin | Trevor Pesout | Ryan Lorig-Roach | Marina Haukness | Vania Costa | Melanie Sorensen | Katherine M. Munson | K. M. Munson | Simon Mayes
[1] Timothy B. Stockwell,et al. The Diploid Genome Sequence of an Individual Human , 2007, PLoS biology.
[2] Sean R. Eddy,et al. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids , 1998 .
[3] Thomas Colthurst,et al. A universal SNP and small-indel variant caller using deep neural networks , 2018, Nature Biotechnology.
[4] David Haussler,et al. Cactus: Algorithms for genome multiple sequence alignment. , 2011, Genome research.
[5] Bronwen L. Aken,et al. GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.
[6] Gabor T. Marth,et al. A global reference for human genetic variation , 2015, Nature.
[7] Evan E. Eichler,et al. An assessment of the sequence gaps: Unfinished business in a finished human genome , 2004, Nature Reviews Genetics.
[8] Jonas Korlach,et al. Discovery and genotyping of structural variation from long-read haploid genome sequence data , 2017, Genome research.
[9] David Haussler,et al. Linear assembly of a human centromere on the Y chromosome , 2018, Nature Biotechnology.
[10] Juan Carlos Castilla-Rubio,et al. Earth BioGenome Project: Sequencing life for the future of life , 2018, Proceedings of the National Academy of Sciences.
[11] Michael C. Schatz,et al. SVCollector: Optimized sample selection for validating and long-read resequencing of structural variants , 2018, bioRxiv.
[12] Michael C. Schatz,et al. Third-generation sequencing and the future of genomics , 2016, bioRxiv.
[13] Ryan L. Collins,et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes , 2017, bioRxiv.
[14] Chunlin Xiao,et al. An open resource for accurately benchmarking small variant and reference calls , 2019, Nature Biotechnology.
[15] Mark Gerstein,et al. GENCODE reference annotation for the human and mouse genomes , 2018, Nucleic Acids Res..
[16] Zev N. Kronenberg,et al. Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads , 2019, bioRxiv.
[17] Benedict Paten,et al. Improved data analysis for the MinION nanopore sequencer , 2015, Nature Methods.
[18] Sergey Koren,et al. Highly-accurate long-read sequencing improves variant detection and assembly of a human genome , 2019, bioRxiv.
[19] J. Dekker,et al. Hi-C: a comprehensive technique to capture the conformation of genomes. , 2012, Methods.
[20] Brendan L. O’Connell,et al. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage , 2015, Genome research.
[21] M. Schatz,et al. Phased diploid genome assembly with single-molecule real-time sequencing , 2016, Nature Methods.
[22] Dmitry Antipov,et al. Versatile genome assembly evaluation with QUAST-LG , 2018, Bioinform..
[23] Sergey Koren,et al. Aggressive assembly of pyrosequencing reads with mates , 2008, Bioinform..
[24] Vitor R. C. Aguiar,et al. Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I Data , 2014, G3: Genes, Genomes, Genetics.
[25] Minsheng Peng,et al. Hybrid assembly of ultra-long Nanopore reads augmented with 10x-Genomics contigs: Demonstrated with a human genome. , 2019, Genomics.
[26] Heng Li,et al. Fast and accurate long-read assembly with wtdbg2 , 2019, Nature Methods.
[27] Leo van Iersel,et al. WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads , 2015, J. Comput. Biol..
[28] Michael C. Schatz,et al. Accurate detection of complex structural variations using single molecule sequencing , 2017, Nature Methods.
[29] Joshua M. Stuart,et al. Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. , 2009, The Journal of heredity.
[30] J D Hayhurst,et al. Single molecule real‐time DNA sequencing of HLA genes at ultra‐high resolution from 126 International HLA and Immunogenetics Workshop cell lines , 2018, HLA.
[31] Richard J. Anderson,et al. Wait-free parallel algorithms for the union-find problem , 1991, STOC '91.
[32] Y. Kamatani,et al. Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing , 2019, Genome Biology.
[33] Heng Li,et al. Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..
[34] Benedict Paten,et al. Haplotype-aware diplotyping from noisy long reads , 2019, Genome Biology.
[35] Inanç Birol,et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species , 2013, GigaScience.
[36] S. Turner,et al. Real-time DNA sequencing from single polymerase molecules. , 2010, Methods in enzymology.
[37] Kunihiko Sadakane,et al. Detecting Superbubbles in Assembly Graphs , 2013, WABI.
[38] Evgeny M. Zdobnov,et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..
[39] S. Koren,et al. Nanopore sequencing and assembly of a human genome with ultra-long reads , 2017, bioRxiv.
[40] Aaron M Wenger,et al. Improved assembly and variant detection of a haploid human genome using single‐molecule, high‐fidelity long reads , 2019, Annals of human genetics.
[41] Niranjan Nagarajan,et al. Fast and accurate de novo genome assembly from long uncorrected reads. , 2017, Genome research.
[42] Shilpa Garg,et al. A graph-based approach to diploid genome assembly , 2018, Bioinform..
[43] Benedict Paten,et al. Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment , 2009, Bioinform..
[44] Sergey Koren,et al. De novo assembly of haplotype-resolved genomes with trio binning , 2018, Nature Biotechnology.
[45] Alexa B. R. McIntyre,et al. Extensive sequencing of seven human genomes to characterize benchmark reference materials , 2015, Scientific Data.
[46] N. Loman,et al. A complete bacterial genome assembled de novo using only nanopore sequencing data , 2015, Nature Methods.
[47] Bradley P. Coe,et al. Genome structural variation discovery and genotyping , 2011, Nature Reviews Genetics.
[48] David Haussler,et al. High-resolution comparative analysis of great ape genomes , 2018, Science.
[49] N. Weisenfeld,et al. Direct determination of diploid genome sequences , 2016, bioRxiv.
[50] Sergey Koren,et al. A robust benchmark for germline structural variant detection , 2019, bioRxiv.
[51] David Haussler,et al. Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis , 2018, Cell.
[52] Andrei Z. Broder,et al. On the resemblance and containment of documents , 1997, Proceedings. Compression and Complexity of SEQUENCES 1997 (Cat. No.97TB100171).
[53] Yu Lin,et al. Assembly of long, error-prone reads using repeat graphs , 2018, Nature Biotechnology.
[54] Luca Antiga,et al. Automatic differentiation in PyTorch , 2017 .
[55] Lakhmi C. Jain,et al. Recurrent Neural Networks: Design and Applications , 1999 .
[56] Ian T. Fiddes. Comparative Annotation Toolkit (CAT) - Simultaneous Clade and Personal Genome Annotation , 2018, Genome research.
[57] Christopher J. Lee,et al. Multiple sequence alignment using partial order graphs , 2002, Bioinform..
[58] Kenny Q. Ye,et al. An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.
[59] J. Landolin,et al. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing , 2014, Nature Biotechnology.
[60] S. Koren,et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.
[61] S. Salzberg,et al. Versatile and open software for comparing large genomes , 2004, Genome Biology.
[62] W. Kloosterman,et al. From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy , 2018, Genome Biology.
[63] Peter M Lansdorp,et al. Strand-seq: a unifying tool for studies of chromosome segregation. , 2013, Seminars in cell & developmental biology.