Filters








13,989 Hits in 5.0 sec

Assembly of Long Error-Prone Reads Using Repeat Graphs [article]

Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel Pevzner
2018 bioRxiv   pre-print
However, most algorithms for assembling long error-prone reads use an alternative overlap-layout-consensus (OLC) approach that does not provide a repeat characterization.  ...  We present the Flye algorithm for constructing the A-Bruijn (assembly) graph from long error-prone reads, that, in contrast to the k-mer-based de Bruijn graph, assembles genomes using an alignment-based  ...  The supplementary files, including the assemblies generated by Flye are available at https://doi.org/10.5281/zenodo.1143753.  ... 
doi:10.1101/247148 fatcat:qzlfzaakajczhdefxrf6t6xaqi

Assembly of long error-prone reads using de Bruijn graphs

Yu Lin, Jeffrey Yuan, Mikhail Kolmogorov, Max W. Shen, Mark Chaisson, Pavel A. Pevzner
2016 Proceedings of the National Academy of Sciences of the United States of America  
The recent breakthroughs in assembling long error-prone reads were based on the overlap-layout-consensus (OLC) approach and did not utilize the strengths of the alternative de Bruijn graph approach to  ...  error-prone reads.  ...  assemblies; and Alexey Gurevich for his help with QUAST and AntiSmash.  ... 
doi:10.1073/pnas.1604560113 pmid:27956617 pmcid:PMC5206522 fatcat:w7o44agzuvckndtr7dut6zjcgi

De novo fragment assembly with short mate-paired reads: Does the read length matter?

M. J. Chaisson, D. Brinza, P. A. Pevzner
2008 Genome Research  
We are grateful to Ronan O'Malley and Joseph Ecker for providing us with the BAC reads.  ...  Assembling error-prone reads (error-correction by threading) Each read corresponds to a unique read path in the de Bruijn graph representing the sequence of the read.  ...  This operation generates the set of extremely accurate (nearly error-free) read prefixes. • Constructing the repeat graph on error corrected prefixes using k-mers. • Simplifying the repeat graph after  ... 
doi:10.1101/gr.079053.108 pmid:19056694 pmcid:PMC2652199 fatcat:5447bmmkkvdhrkkbqxudrsifc4

Assembly of Long Error-Prone Reads Using de Bruijn Graphs [article]

Yu Lin, Jeffrey Yuan, Mikhail Kolmogorov, Max W. Shen, Pavel A. Pevzner
2016 bioRxiv   pre-print
for assembling long error-prone reads.  ...  Below we show how to generalize de Bruijn graphs to assemble long error-prone reads and describe the ABruijn assembler, which results in more accurate genome reconstructions than the existing state-of-the-art  ...  Acknowledgments We are grateful to Mark Chaisson for his help with the PBcR and Quiver analysis as well as to Bahar Behsaz, Anton Korobeinikov, Mihai Pop, and Glenn Tesler for their many useful comments  ... 
doi:10.1101/048413 fatcat:uu54m5dihrbhzcftxxjuawo6ha

HINGE: long-read assembly achieves optimal repeat resolution

Govinda M. Kamath, Ilan Shomorony, Fei Xia, Thomas A. Courtade, David N. Tse
2017 Genome Research  
Long-read sequencing technologies have the potential to produce gold-standard de novo genome assemblies, but fully exploiting error-prone reads to resolve repeats remains a challenge.  ...  As a result, HINGE combines the error resilience of overlap-based assemblers with repeat-resolution capabilities of de Bruijn graph assemblers.  ...  Acknowledgments The authors thank Shoudan Liang and Jason Chin of Pacific Biosciences for useful discussions and Lior Pachter of UC Berkeley for helpful comments and suggestions during the preparation  ... 
doi:10.1101/gr.216465.116 pmid:28320918 pmcid:PMC5411769 fatcat:4x2myklanjbnhn5436vki4fzk4

Extending rnaSPAdes functionality for hybrid transcriptome assembly

Andrey D. Prjibelski, Giuseppe D. Puglia, Dmitry Antipov, Elena Bushmanova, Daniela Giordano, Alla Mikheenko, Domenico Vitale, Alla Lapidus
2020 BMC Bioinformatics  
out from long error-prone reads.  ...  To evaluate the benefit of using long RNA reads we selected several datasets containing both Illumina and Iso-seq or Oxford Nanopore Technologies (ONT) reads.  ...  Acknowledgments For uploading their data to public databases the authors would like to thank Nick Loman and other contributors of Oxford Nanopore RNA sequencing project, as well as the staff of following  ... 
doi:10.1186/s12859-020-03614-2 pmid:32703149 fatcat:6mfr5etwpnbotklt36lb6dstbu

mosaicFlye: Resolving long mosaic repeats using long error-prone reads [article]

Anton Bankevich, Pavel Pevzner
2020 bioRxiv   pre-print
Long-read technologies revolutionized genome assembly and enabled resolution of bridged repeats (i.e., repeats that are spanned by some reads) in various genomes.  ...  Moreover, the challenge of resolving unbridged repeats is not limited to eukaryotic genomes but also impairs assemblies of long repeats in bacterial genomes and metagenomes.  ...  In contrast, long-read assemblers face difficulties resolving such repeats since repeat copies with 3% divergence are difficult to distinguish using the error-prone reads that have error rates exceeding  ... 
doi:10.1101/2020.01.15.908285 fatcat:nzfhvzk24factlkx4l66plepfy

Extending rnaSPAdes functionality for hybrid transcriptome assembly [article]

Andrey D. Prjibelski, Giuseppe D. Puglia, Dmitry Antipov, Elena Bushmanova, Daniela Giordano, Alla Mikheenko, Domenico Vitale, Alla Lapidus
2020 bioRxiv   pre-print
carried out from long error-prone reads.  ...  Conclusion: To evaluate the benefit of using long RNA reads we selected several datasets containing both Illumina and Iso-seq or Oxford Nanopore Technologies (ONT) reads.  ...  Acknowledgments For uploading their data to public databases the authors would like to thank Nick Loman and other contributors of Oxford Nanopore RNA sequencing project, as well as the staff of following  ... 
doi:10.1101/2020.01.24.918482 fatcat:jdcn7d5vmrekdkmsjwt3z6b6ju

Short read fragment assembly of bacterial genomes

M. J. Chaisson, P. A. Pevzner
2008 Genome Research  
Huang et al. (2003) and Jaffe et al. (2003) for efficient construction of the repeat graph even in the simple case of SBH "reads."  ...  advantages of the Eulerian path approach over the "overlap-layout-consensus" approach for fragment assembly.  ...  We thank Michael Egholm and James Knight for providing us with 454 reads and assemblies and helpful discussions about pyrosequencing reads.  ... 
doi:10.1101/gr.7088808 pmid:18083777 pmcid:PMC2203630 fatcat:drv2xvemkbgchgvbeni3ufhyji

Building near-complete plant genomes

Todd P Michael, Robert VanBuren
2020 Current opinion in plant biology  
to assemble.  ...  Single molecule reads can now exceed megabases in length, providing unprecedented opportunities to untangle genomic regions missed by short read technologies.  ...  Draft long read assemblies have residual errors and must be polished using a combination of high-coverage long read and/or short read data.  ... 
doi:10.1016/j.pbi.2019.12.009 pmid:31981929 fatcat:iidgialiczer5j6mdxho3tsy2i

metaSPAdes: a new versatile de novo metagenomics assembler [article]

Sergey Nurk, Dmitry Meleshko, Anton Korobeynikov, Pavel Pevzner
2016 arXiv   pre-print
that addresses the challenge of metagenome analysis and capitalizes on computational ideas that proved to be useful in assemblies of single cells and highly polymorphic diploid genomes.  ...  While metagenomics has emerged as a technology of choice for analyzing bacterial populations, assembly of metagenomic data remains difficult thus stifling biological discoveries. metaSPAdes is a new assembler  ...  We are grateful to Chris Dupont, Mihai Pop, and Bahar Behsaz for useful comments. We are also grateful to Alla Lapidus, who brought our attention to the field of metagenomics.  ... 
arXiv:1604.03071v2 fatcat:og3mxwoxbrfdnl5wfhfhnyltiy

HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution [article]

Govinda M Kamath, Ilan Shomorony, Fei Xia, Thomas A Courtade, David N Tse
2016 bioRxiv   pre-print
Long-read sequencing technologies have the potential to produce gold-standard de novo genome assemblies, but fully exploiting error-prone reads to resolve repeats remains a challenge.  ...  As a result, HINGE combines the error resilience of overlap-based assemblers with repeat-resolution capabilities of de Bruijn graph assemblers.  ...  ACKNOWLEDGEMENTS The authors would like to thank Shoudan Liang and Jason Chin of Pacific Biosciences for useful discussions, and Lior Pachter of UC Berkeley for helpful comments and suggestions during  ... 
doi:10.1101/062117 fatcat:dw5mtku4ujbidhzwo5r2u4a2zm

Assembling Long Accurate Reads Using de Bruijn Graphs [article]

Anton Bankevich, Andrey V Bzikadze, Mikhail Kolmogorov, Pavel Pevzner
2020 bioRxiv   pre-print
LJA genome assembler that error-corrects HiFi reads and uses jumboDB to construct the de Bruijn graph on the error-corrected reads.  ...  assembly of the human genome using the alternative string graph assembly approach.  ...  Assembling cen6 using shorter HiFi reads is challenging since it contains long nearly identical repeats.  ... 
doi:10.1101/2020.12.10.420448 fatcat:euaezkb5czfmpfhdjfj2vsjgiq

The String Decomposition Problem and its Applications to Centromere Assembly [article]

Tatiana Dvorkina, Andrey V. Bzikadze, Pavel A. Pevzner
2019 bioRxiv   pre-print
Recent attempts to assemble long tandem repeats (such as multi-megabase long centromeres) faced the challenge of accurate translation of long error-prone reads from the nucleotide alphabet into the alphabet  ...  The accurate translation of each read into a monomer alphabet turns centromere assembly into a more tractable problem than the notoriously difficult problem of assembling centromeres in the nucleotide  ...  Acknowledgements We are grateful to Ivan Alexandrov, Karen Miga, and Alla Mikheenko for many useful insights. This work was supported by St. Petersburg State University, St.  ... 
doi:10.1101/2019.12.26.888685 fatcat:gjv5lse7ifevxgcpmthd5wbwhy

Unicycler: resolving bacterial genome assemblies from short and long sequencing reads [article]

Ryan R. Wick, Louise M. Judd, Claire L. Gorrie, Kathryn E. Holt
2016 biorxiv/medrxiv   pre-print
Unicycler builds an initial assembly graph from short reads using the de novo assembler SPAdes and then simplifies the graph using information from short and long reads.  ...  Unicycler utilises a novel semi-global aligner, which is used to align long reads to the assembly graph.  ...  Theoretical analyses of assembly show that error-prone reads are nearly as informative as error-free reads, suggesting that read accuracy is less important than length [43, 44] .  ... 
doi:10.1101/096412 fatcat:fibbfptvljdbzfobdeeikd2l3y
« Previous Showing results 1 — 15 out of 13,989 results