Guillaume Holley, Doruk Beyter, Helga Ingimundardottir, Peter L Møller, Snædis Kristmundsdottir, Hannes P Eggertsson, Bjarni V Halldorsson. Genome Biol 2021
Times Cited: 5
Times Cited: 5
Times Cited
Times Co-cited
Similarity
Assembly of long, error-prone reads using repeat graphs.
Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A Pevzner. Nat Biotechnol 2019
Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A Pevzner. Nat Biotechnol 2019
100
NanoPack: visualizing and processing long-read sequencing data.
Wouter De Coster, Svenn D'Hert, Darrin T Schultz, Marc Cruts, Christine Van Broeckhoven. Bioinformatics 2018
Wouter De Coster, Svenn D'Hert, Darrin T Schultz, Marc Cruts, Christine Van Broeckhoven. Bioinformatics 2018
80
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.
Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, Marina Haukness, Hugh E Olsen, Colleen Bosworth, Joel Armstrong, Kristof Tigyi, Nicholas Maurer, Sergey Koren,[...]. Nat Biotechnol 2020
Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, Marina Haukness, Hugh E Olsen, Colleen Bosworth, Joel Armstrong, Kristof Tigyi, Nicholas Maurer, Sergey Koren,[...]. Nat Biotechnol 2020
60
Nanopore sequencing and assembly of a human genome with ultra-long reads.
Miten Jain, Sergey Koren, Karen H Miga, Josh Quick, Arthur C Rand, Thomas A Sasani, John R Tyson, Andrew D Beggs, Alexander T Dilthey, Ian T Fiddes,[...]. Nat Biotechnol 2018
Miten Jain, Sergey Koren, Karen H Miga, Josh Quick, Arthur C Rand, Thomas A Sasani, John R Tyson, Andrew D Beggs, Alexander T Dilthey, Ian T Fiddes,[...]. Nat Biotechnol 2018
60
Fast and accurate de novo genome assembly from long uncorrected reads.
Robert Vaser, Ivan Sović, Niranjan Nagarajan, Mile Šikić. Genome Res 2017
Robert Vaser, Ivan Sović, Niranjan Nagarajan, Mile Šikić. Genome Res 2017
60
The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community.
Miten Jain, Hugh E Olsen, Benedict Paten, Mark Akeson. Genome Biol 2016
Miten Jain, Hugh E Olsen, Benedict Paten, Mark Akeson. Genome Biol 2016
40
Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
40
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
Sergey Koren, Brian P Walenz, Konstantin Berlin, Jason R Miller, Nicholas H Bergman, Adam M Phillippy. Genome Res 2017
Sergey Koren, Brian P Walenz, Konstantin Berlin, Jason R Miller, Nicholas H Bergman, Adam M Phillippy. Genome Res 2017
40
Hybrid error correction and de novo assembly of single-molecule sequencing reads.
Sergey Koren, Michael C Schatz, Brian P Walenz, Jeffrey Martin, Jason T Howard, Ganeshkumar Ganapathy, Zhong Wang, David A Rasko, W Richard McCombie, Erich D Jarvis,[...]. Nat Biotechnol 2012
Sergey Koren, Michael C Schatz, Brian P Walenz, Jeffrey Martin, Jason T Howard, Ganeshkumar Ganapathy, Zhong Wang, David A Rasko, W Richard McCombie, Erich D Jarvis,[...]. Nat Biotechnol 2012
40
Versatile and open software for comparing large genomes.
Stefan Kurtz, Adam Phillippy, Arthur L Delcher, Michael Smoot, Martin Shumway, Corina Antonescu, Steven L Salzberg. Genome Biol 2004
Stefan Kurtz, Adam Phillippy, Arthur L Delcher, Michael Smoot, Martin Shumway, Corina Antonescu, Steven L Salzberg. Genome Biol 2004
40
A comparative evaluation of hybrid error correction methods for error-prone long reads.
Shuhua Fu, Anqi Wang, Kin Fai Au. Genome Biol 2019
Shuhua Fu, Anqi Wang, Kin Fai Au. Genome Biol 2019
40
FMLRC: Hybrid long read error correction using an FM-index.
Jeremy R Wang, James Holt, Leonard McMillan, Corbin D Jones. BMC Bioinformatics 2018
Jeremy R Wang, James Holt, Leonard McMillan, Corbin D Jones. BMC Bioinformatics 2018
40
Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
Bruce J Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K Young,[...]. PLoS One 2014
Bruce J Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K Young,[...]. PLoS One 2014
40
Characterization of individual polynucleotide molecules using a membrane channel.
J J Kasianowicz, E Brandin, D Branton, D W Deamer. Proc Natl Acad Sci U S A 1996
J J Kasianowicz, E Brandin, D Branton, D W Deamer. Proc Natl Acad Sci U S A 1996
40
MinIONQC: fast and simple quality control for MinION sequencing data.
R Lanfear, M Schalamun, D Kainer, W Wang, B Schwessinger. Bioinformatics 2019
R Lanfear, M Schalamun, D Kainer, W Wang, B Schwessinger. Bioinformatics 2019
40
TRiCoLOR: tandem repeat profiling using whole-genome long-read sequencing data.
Davide Bolognini, Alberto Magi, Vladimir Benes, Jan O Korbel, Tobias Rausch. Gigascience 2020
Davide Bolognini, Alberto Magi, Vladimir Benes, Jan O Korbel, Tobias Rausch. Gigascience 2020
40
Phased diploid genome assembly with single-molecule real-time sequencing.
Chen-Shan Chin, Paul Peluso, Fritz J Sedlazeck, Maria Nattestad, Gregory T Concepcion, Alicia Clum, Christopher Dunn, Ronan O'Malley, Rosa Figueroa-Balderas, Abraham Morales-Cruz,[...]. Nat Methods 2016
Chen-Shan Chin, Paul Peluso, Fritz J Sedlazeck, Maria Nattestad, Gregory T Concepcion, Alicia Clum, Christopher Dunn, Ronan O'Malley, Rosa Figueroa-Balderas, Abraham Morales-Cruz,[...]. Nat Methods 2016
40
Telomere-to-telomere assembly of a complete human X chromosome.
Karen H Miga, Sergey Koren, Arang Rhie, Mitchell R Vollger, Ariel Gershman, Andrey Bzikadze, Shelise Brooks, Edmund Howe, David Porubsky, Glennis A Logsdon,[...]. Nature 2020
Karen H Miga, Sergey Koren, Arang Rhie, Mitchell R Vollger, Ariel Gershman, Andrey Bzikadze, Shelise Brooks, Edmund Howe, David Porubsky, Glennis A Logsdon,[...]. Nature 2020
40
Targeted nanopore sequencing with Cas9-guided adapter ligation.
Timothy Gilpatrick, Isac Lee, James E Graham, Etienne Raimondeau, Rebecca Bowen, Andrew Heron, Bradley Downs, Saraswati Sukumar, Fritz J Sedlazeck, Winston Timp. Nat Biotechnol 2020
Timothy Gilpatrick, Isac Lee, James E Graham, Etienne Raimondeau, Rebecca Bowen, Andrew Heron, Bradley Downs, Saraswati Sukumar, Fritz J Sedlazeck, Winston Timp. Nat Biotechnol 2020
40
NanoVar: accurate characterization of patients' genomic structural variants using low-depth nanopore sequencing.
Cheng Yong Tham, Roberto Tirado-Magallanes, Yufen Goh, Melissa J Fullwood, Bryan T H Koh, Wilson Wang, Chin Hin Ng, Wee Joo Chng, Alexandre Thiery, Daniel G Tenen,[...]. Genome Biol 2020
Cheng Yong Tham, Roberto Tirado-Magallanes, Yufen Goh, Melissa J Fullwood, Bryan T H Koh, Wilson Wang, Chin Hin Ng, Wee Joo Chng, Alexandre Thiery, Daniel G Tenen,[...]. Genome Biol 2020
40
Multi-platform discovery of haplotype-resolved structural variation in human genomes.
Mark J P Chaisson, Ashley D Sanders, Xuefang Zhao, Ankit Malhotra, David Porubsky, Tobias Rausch, Eugene J Gardner, Oscar L Rodriguez, Li Guo, Ryan L Collins,[...]. Nat Commun 2019
Mark J P Chaisson, Ashley D Sanders, Xuefang Zhao, Ankit Malhotra, David Porubsky, Tobias Rausch, Eugene J Gardner, Oscar L Rodriguez, Li Guo, Ryan L Collins,[...]. Nat Commun 2019
40
Adaptive seeds tame genomic sequence comparison.
Szymon M Kiełbasa, Raymond Wan, Kengo Sato, Paul Horton, Martin C Frith. Genome Res 2011
Szymon M Kiełbasa, Raymond Wan, Kengo Sato, Paul Horton, Martin C Frith. Genome Res 2011
40
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm.
Haoyu Cheng, Gregory T Concepcion, Xiaowen Feng, Haowen Zhang, Heng Li. Nat Methods 2021
Haoyu Cheng, Gregory T Concepcion, Xiaowen Feng, Haowen Zhang, Heng Li. Nat Methods 2021
40
BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files.
Alexander Payne, Nadine Holmes, Vardhman Rakyan, Matthew Loose. Bioinformatics 2019
Alexander Payne, Nadine Holmes, Vardhman Rakyan, Matthew Loose. Bioinformatics 2019
40
Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing.
Peter Edge, Vikas Bansal. Nat Commun 2019
Peter Edge, Vikas Bansal. Nat Commun 2019
40
SVIM: structural variant identification using mapped long reads.
David Heller, Martin Vingron. Bioinformatics 2019
David Heller, Martin Vingron. Bioinformatics 2019
40
metaFlye: scalable long-read metagenome assembly using repeat graphs.
Mikhail Kolmogorov, Derek M Bickhart, Bahar Behsaz, Alexey Gurevich, Mikhail Rayko, Sung Bong Shin, Kristen Kuhn, Jeffrey Yuan, Evgeny Polevikov, Timothy P L Smith,[...]. Nat Methods 2020
Mikhail Kolmogorov, Derek M Bickhart, Bahar Behsaz, Alexey Gurevich, Mikhail Rayko, Sung Bong Shin, Kristen Kuhn, Jeffrey Yuan, Evgeny Polevikov, Timothy P L Smith,[...]. Nat Methods 2020
40
Accurate detection of complex structural variations using single-molecule sequencing.
Fritz J Sedlazeck, Philipp Rescheneder, Moritz Smolka, Han Fang, Maria Nattestad, Arndt von Haeseler, Michael C Schatz. Nat Methods 2018
Fritz J Sedlazeck, Philipp Rescheneder, Moritz Smolka, Han Fang, Maria Nattestad, Arndt von Haeseler, Michael C Schatz. Nat Methods 2018
40
Performance of neural network basecalling tools for Oxford Nanopore sequencing.
Ryan R Wick, Louise M Judd, Kathryn E Holt. Genome Biol 2019
Ryan R Wick, Louise M Judd, Kathryn E Holt. Genome Biol 2019
40
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies.
Peter Edge, Vineet Bafna, Vikas Bansal. Genome Res 2017
Peter Edge, Vineet Bafna, Vikas Bansal. Genome Res 2017
40
lra: A long read aligner for sequences and contigs.
Jingwen Ren, Mark J P Chaisson. PLoS Comput Biol 2021
Jingwen Ren, Mark J P Chaisson. PLoS Comput Biol 2021
40
GraphAligner: rapid and versatile sequence-to-graph alignment.
Mikko Rautiainen, Tobias Marschall. Genome Biol 2020
Mikko Rautiainen, Tobias Marschall. Genome Biol 2020
40
Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads.
Carolin A Müller, Michael A Boemo, Paolo Spingardi, Benedikt M Kessler, Skirmantas Kriaucionis, Jared T Simpson, Conrad A Nieduszynski. Nat Methods 2019
Carolin A Müller, Michael A Boemo, Paolo Spingardi, Benedikt M Kessler, Skirmantas Kriaucionis, Jared T Simpson, Conrad A Nieduszynski. Nat Methods 2019
40
Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION.
Melissa Leija-Salazar, Fritz J Sedlazeck, Marco Toffoli, Stephen Mullin, Katya Mokretar, Maria Athanasopoulou, Aimee Donald, Reena Sharma, Derralynn Hughes, Anthony H V Schapira,[...]. Mol Genet Genomic Med 2019
Melissa Leija-Salazar, Fritz J Sedlazeck, Marco Toffoli, Stephen Mullin, Katya Mokretar, Maria Athanasopoulou, Aimee Donald, Reena Sharma, Derralynn Hughes, Anthony H V Schapira,[...]. Mol Genet Genomic Med 2019
40
Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing.
Isac Lee, Roham Razaghi, Timothy Gilpatrick, Michael Molnar, Ariel Gershman, Norah Sadowski, Fritz J Sedlazeck, Kasper D Hansen, Jared T Simpson, Winston Timp. Nat Methods 2020
Isac Lee, Roham Razaghi, Timothy Gilpatrick, Michael Molnar, Ariel Gershman, Norah Sadowski, Fritz J Sedlazeck, Kasper D Hansen, Jared T Simpson, Winston Timp. Nat Methods 2020
40
Long-read-based human genomic structural variation detection with cuteSV.
Tao Jiang, Yongzhuang Liu, Yue Jiang, Junyi Li, Yan Gao, Zhe Cui, Yadong Liu, Bo Liu, Yadong Wang. Genome Biol 2020
Tao Jiang, Yongzhuang Liu, Yue Jiang, Junyi Li, Yan Gao, Zhe Cui, Yadong Liu, Bo Liu, Yadong Wang. Genome Biol 2020
40
NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION.
Arne De Roeck, Wouter De Coster, Liene Bossaerts, Rita Cacace, Tim De Pooter, Jasper Van Dongen, Svenn D'Hert, Peter De Rijk, Mojca Strazisar, Christine Van Broeckhoven,[...]. Genome Biol 2019
Arne De Roeck, Wouter De Coster, Liene Bossaerts, Rita Cacace, Tim De Pooter, Jasper Van Dongen, Svenn D'Hert, Peter De Rijk, Mojca Strazisar, Christine Van Broeckhoven,[...]. Genome Biol 2019
40
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.
Heng Li. Bioinformatics 2016
Heng Li. Bioinformatics 2016
40
BUSCO: Assessing Genome Assembly and Annotation Completeness.
Mathieu Seppey, Mosè Manni, Evgeny M Zdobnov. Methods Mol Biol 2019
Mathieu Seppey, Mosè Manni, Evgeny M Zdobnov. Methods Mol Biol 2019
20
Genome assembly has a major impact on gene content: a comparison of annotation in two Bos taurus assemblies.
Liliana Florea, Alexander Souvorov, Theodore S Kalbfleisch, Steven L Salzberg. PLoS One 2011
Liliana Florea, Alexander Souvorov, Theodore S Kalbfleisch, Steven L Salzberg. PLoS One 2011
20
Circos: an information aesthetic for comparative genomics.
Martin Krzywinski, Jacqueline Schein, Inanç Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J Jones, Marco A Marra. Genome Res 2009
Martin Krzywinski, Jacqueline Schein, Inanç Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J Jones, Marco A Marra. Genome Res 2009
20
i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets.
Sebastian Proost, Jan Fostier, Dieter De Witte, Bart Dhoedt, Piet Demeester, Yves Van de Peer, Klaas Vandepoele. Nucleic Acids Res 2012
Sebastian Proost, Jan Fostier, Dieter De Witte, Bart Dhoedt, Piet Demeester, Yves Van de Peer, Klaas Vandepoele. Nucleic Acids Res 2012
20
The value of new genome references.
Kim C Worley, Stephen Richards, Jeffrey Rogers. Exp Cell Res 2017
Kim C Worley, Stephen Richards, Jeffrey Rogers. Exp Cell Res 2017
20
Carbon translocation from a plant to an insect-pathogenic endophytic fungus.
Scott W Behie, Camila C Moreira, Irina Sementchoukova, Larissa Barelli, Paul M Zelisko, Michael J Bidochka. Nat Commun 2017
Scott W Behie, Camila C Moreira, Irina Sementchoukova, Larissa Barelli, Paul M Zelisko, Michael J Bidochka. Nat Commun 2017
20
SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation.
Wei Shen, Shuai Le, Yan Li, Fuquan Hu. PLoS One 2016
Wei Shen, Shuai Le, Yan Li, Fuquan Hu. PLoS One 2016
20
The evolution of genome mining in microbes - a review.
Nadine Ziemert, Mohammad Alanjary, Tilmann Weber. Nat Prod Rep 2016
Nadine Ziemert, Mohammad Alanjary, Tilmann Weber. Nat Prod Rep 2016
20
OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species.
Ling Xu, Zhaobin Dong, Lu Fang, Yongjiang Luo, Zhaoyuan Wei, Hailong Guo, Guoqing Zhang, Yong Q Gu, Devin Coleman-Derr, Qingyou Xia,[...]. Nucleic Acids Res 2019
Ling Xu, Zhaobin Dong, Lu Fang, Yongjiang Luo, Zhaoyuan Wei, Hailong Guo, Guoqing Zhang, Yong Q Gu, Devin Coleman-Derr, Qingyou Xia,[...]. Nucleic Acids Res 2019
20
Processes of fungal proteome evolution and gain of function: gene duplication and domain rearrangement.
Inbar Cohen-Gihon, Roded Sharan, Ruth Nussinov. Phys Biol 2011
Inbar Cohen-Gihon, Roded Sharan, Ruth Nussinov. Phys Biol 2011
20
Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.