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Assembly of long error-prone reads using de Bruijn graphs

Yu Lin, Jeffrey Yuan, Mikhail Kolmogorov, Max W. Shen, Mark Chaisson, Pavel A. Pevzner
<span title="2016-12-12">2016</span> <i title="Proceedings of the National Academy of Sciences"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nvtuoas5pbdsllkntnhizy4f4q" style="color: black;">Proceedings of the National Academy of Sciences of the United States of America</a> </i> &nbsp;
We show how to generalize de Bruijn graphs for assembling long error-prone reads and describe the ABruijn assembler, which combines the de Bruijn graph and the OLC approaches and results in accurate genome  ...  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  ...  assemblies; and Alexey Gurevich for his help with QUAST and AntiSmash.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1604560113">doi:10.1073/pnas.1604560113</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27956617">pmid:27956617</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5206522/">pmcid:PMC5206522</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/w7o44agzuvckndtr7dut6zjcgi">fatcat:w7o44agzuvckndtr7dut6zjcgi</a> </span>
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Assembly of Long Error-Prone Reads Using de Bruijn Graphs [article]

Yu Lin, Jeffrey Yuan, Mikhail Kolmogorov, Max W. Shen, Pavel A. Pevzner
<span title="2016-04-13">2016</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
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  ...  strengths of the alternative de Bruijn graph approach to genome assembly.  ...  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  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/048413">doi:10.1101/048413</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uu54m5dihrbhzcftxxjuawo6ha">fatcat:uu54m5dihrbhzcftxxjuawo6ha</a> </span>
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Short read fragment assembly of bacterial genomes

M. J. Chaisson, P. A. Pevzner
<span title="2008-02-01">2008</span> <i title="Cold Spring Harbor Laboratory"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nwro4atxwbec5pfkpfslaxbdae" style="color: black;">Genome Research</a> </i> &nbsp;
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.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.7088808">doi:10.1101/gr.7088808</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18083777">pmid:18083777</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2203630/">pmcid:PMC2203630</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/drv2xvemkbgchgvbeni3ufhyji">fatcat:drv2xvemkbgchgvbeni3ufhyji</a> </span>
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De novo fragment assembly with short mate-paired reads: Does the read length matter?

M. J. Chaisson, D. Brinza, P. A. Pevzner
<span title="2008-12-03">2008</span> <i title="Cold Spring Harbor Laboratory"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nwro4atxwbec5pfkpfslaxbdae" style="color: black;">Genome Research</a> </i> &nbsp;
We are grateful to Ronan O'Malley and Joseph Ecker for providing us with the BAC reads.  ...  We thank Dirk Evers, Klaus Maisinger, and Jacques Retief for insightful discussions about the Illumina technology and to Xiaohua Huang and Eric Roller for many discussions on emerging next-generation sequencing  ...  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.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.079053.108">doi:10.1101/gr.079053.108</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19056694">pmid:19056694</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2652199/">pmcid:PMC2652199</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5447bmmkkvdhrkkbqxudrsifc4">fatcat:5447bmmkkvdhrkkbqxudrsifc4</a> </span>
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Assembling Long Accurate Reads Using de Bruijn Graphs [article]

Anton Bankevich, Andrey V Bzikadze, Mikhail Kolmogorov, Pavel Pevzner
<span title="2020-12-11">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
LJA genome assembler that error-corrects HiFi reads and uses jumboDB to construct the de Bruijn graph on the error-corrected reads.  ...  Although the de Bruijn graphs represent the basis of many genome assemblers, it remains unclear how to construct these graphs for large genomes and large k-mer sizes.  ...  long k -mers from the genome typically do not even occur in error-prone reads, it seemed unlikely that the de Bruijn graph approach may assemble such reads.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.12.10.420448">doi:10.1101/2020.12.10.420448</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/euaezkb5czfmpfhdjfj2vsjgiq">fatcat:euaezkb5czfmpfhdjfj2vsjgiq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210428223246/https://www.biorxiv.org/content/biorxiv/early/2020/12/11/2020.12.10.420448.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f0/58/f0585ad2222bdb83cfa3600085bdb92b77e6091f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.12.10.420448"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

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

Anton Bankevich, Pavel Pevzner
<span title="2020-01-16">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
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.  ...  The (potentially error-prone) gap Figure 2 : 2 A genome with three copies of a mosaic repeat (left), its de Bruijn graph (middle top), its repeat graph (right top), alignment of reads to the de Bruijn  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.01.15.908285">doi:10.1101/2020.01.15.908285</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nzfhvzk24factlkx4l66plepfy">fatcat:nzfhvzk24factlkx4l66plepfy</a> </span>
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Updating benchtop sequencing performance comparison

Sebastian Jünemann, Fritz Joachim Sedlazeck, Karola Prior, Andreas Albersmeier, Uwe John, Jörn Kalinowski, Alexander Mellmann, Alexander Goesmann, Arndt von Haeseler, Jens Stoye, Dag Harmsen
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/t2bqrmk7orfmxpqzqwiiyjwide" style="color: black;">Nature Biotechnology</a> </i> &nbsp;
Assembly of Larger Genomes Since ABySS uses parallelization and de Bruijn graphs, it can be used for de novo assembly of larger genomes.  ...  De Bruijn Graphs Because overlap graphs do not scale well with increasing numbers of reads, most assemblers for next-generation sequencing use de Bruijn graphs.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nbt.2522">doi:10.1038/nbt.2522</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23563421">pmid:23563421</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2u4gutr32jdwha736o5f47m42i">fatcat:2u4gutr32jdwha736o5f47m42i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430144431/https://www.illumina.com/Documents/products/technotes/technote_denovo_assembly_ecoli.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ff/bf/ffbf8a90a2e37dccca79e21a6e84b3d4a3dc77ce.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nbt.2522"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a>

SEQuel: improving the accuracy of genome assemblies

R. Ronen, C. Boucher, H. Chitsaz, P. Pevzner
<span title="2012-06-11">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Fundamental to the algorithm behind SEQuel is the positional de Bruijn graph, a graph structure that models k-mers within reads while incorporating the approximate positions of reads into the model.  ...  Availability: SEQuel can be used as a post-processing step in combination with any NGS assembler and is freely available at  ...  Funding: CB and PP were funded by National Institutes of Health (grant 3P41RR024851-02S1) for the duration of this research. RR was funded by National Science Foundation (grant CCF-1115206).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts219">doi:10.1093/bioinformatics/bts219</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22689760">pmid:22689760</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3371851/">pmcid:PMC3371851</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/h2fzzwwsfndnneccdb4pkhqq3y">fatcat:h2fzzwwsfndnneccdb4pkhqq3y</a> </span>
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HINGE: long-read assembly achieves optimal repeat resolution

Govinda M. Kamath, Ilan Shomorony, Fei Xia, Thomas A. Courtade, David N. Tse
<span title="2017-03-20">2017</span> <i title="Cold Spring Harbor Laboratory"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nwro4atxwbec5pfkpfslaxbdae" style="color: black;">Genome Research</a> </i> &nbsp;
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  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.216465.116">doi:10.1101/gr.216465.116</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28320918">pmid:28320918</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5411769/">pmcid:PMC5411769</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4x2myklanjbnhn5436vki4fzk4">fatcat:4x2myklanjbnhn5436vki4fzk4</a> </span>
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Fragment assembly with double-barreled data

P. A. Pevzner, H. Tang
<span title="2001-06-01">2001</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
For long nearly-perfect repeats this question is notoriously difficult and some copies of such repeats may be "lost" in genomic assemblies.  ...  However, the limits of these algorithms are being tested in the era of genomic sequencing and it is not clear whether they are the best choice for large-scale assemblies.  ...  We are grateful to Michael Fonstein, Eugene Goltsman, Zufar Mulyukov, Julian Parkhill, Alexei Sorokine, and Michael Waterman for useful discussions and providing sequencing data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/17.suppl_1.s225">doi:10.1093/bioinformatics/17.suppl_1.s225</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11473013">pmid:11473013</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r7vcy6yhffbezowzs6rexndy6e">fatcat:r7vcy6yhffbezowzs6rexndy6e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20140109105624/http://bioinformatics.oxfordjournals.org/content/17/suppl_1/S225.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3e/41/3e41a75e5988b73d186d22daf5b2a1b174509fac.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/17.suppl_1.s225"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

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

Sergey Nurk, Dmitry Meleshko, Anton Korobeynikov, Pavel Pevzner
<span title="2016-08-01">2016</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
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.  ...  We benchmark metaSPAdes against other state-of-the-art metagenome assemblers across diverse da-tasets and demonstrate that it results in high-quality assemblies.  ...  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.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1604.03071v2">arXiv:1604.03071v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/og3mxwoxbrfdnl5wfhfhnyltiy">fatcat:og3mxwoxbrfdnl5wfhfhnyltiy</a> </span>
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Empirical evaluation of methods for de novo genome assembly

Firaol Dida, Gangman Yi
<span title="2021-07-09">2021</span> <i title="PeerJ"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zs2czkfyybggbpvr26rbyxpsjy" style="color: black;">PeerJ Computer Science</a> </i> &nbsp;
We make a thorough comparison of the de novo assembly algorithms to allow new users to clearly understand the assembly algorithms: overlap-layout-consensus and de-Bruijn-graph, string-graph based assembly  ...  We also address the computational efficacy of each algorithm's performance, challenges faced by the assem- bly tools used, and the impact of repeats.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7717/peerj-cs.636">doi:10.7717/peerj-cs.636</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/p5qvfccmdzb2pjje7ylkwedqza">fatcat:p5qvfccmdzb2pjje7ylkwedqza</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210709175800/https://peerj.com/articles/cs-636.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0f/f7/0ff7c1f3ff31fbbbc6dc4437dd15a217d7346079.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7717/peerj-cs.636"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

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

Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel Pevzner
<span title="2018-01-12">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
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  ...  However, most algorithms for assembling long error-prone reads use an alternative overlap-layout-consensus (OLC) approach that does not provide a repeat characterization.  ...  The supplementary files, including the assemblies generated by Flye are available at https://doi.org/10.5281/zenodo.1143753.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/247148">doi:10.1101/247148</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qzlfzaakajczhdefxrf6t6xaqi">fatcat:qzlfzaakajczhdefxrf6t6xaqi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719083159/https://www.biorxiv.org/content/biorxiv/early/2018/01/12/247148.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/33/e0/33e0d96e08f4f88293c850412c2f8831ed27b4a6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/247148"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Toward perfect reads: short reads correction via mapping on compacted de Bruijn graphs [article]

Antoine Limasset, Jean-Francois Flot, Pierre Peterlongo
<span title="2019-02-28">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Results: We propose a new method to correct short reads using de Bruijn graphs, and implement it as a tool called Bcool. As a first step, Bcool constructs a compacted de Bruijn graph from the reads.  ...  Motivations: Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction.  ...  In the LoRDEC approach, this de Bruijn graph is built from highly accurate short reads and used to correct long reads.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/558395">doi:10.1101/558395</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/phdjwwhf3rczrmfoorzxbk33l4">fatcat:phdjwwhf3rczrmfoorzxbk33l4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501034729/https://www.biorxiv.org/content/biorxiv/early/2019/02/28/558395.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1d/61/1d615aba4e5e84e4e9cdc0bf73e4ef7869eb2f1e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/558395"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Reference-free SNP detection: dealing with the data deluge

Richard M Leggett, Dan MacLean
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
Reference-free SNP detection, that is identifying SNPs between samples directly from comparison of primary sequencing data with other primary sequencing data and not to a pre-assembled reference genome  ...  and personal genomics and medicine.  ...  Acknowledgements The authors would like to thank Leighton Pritchard and Burkhard Steuernagel for critical reading of the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-15-s4-s10">doi:10.1186/1471-2164-15-s4-s10</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25056481">pmid:25056481</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4083407/">pmcid:PMC4083407</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5so3edn42fen5comujno7u475m">fatcat:5so3edn42fen5comujno7u475m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830084537/https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-15-S4-S10?site=http://bmcgenomics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b6/d4/b6d408d0d557127bf83b5bc6b079687a9c63bb34.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-15-s4-s10"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4083407" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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