Literature DB >> 33468205

Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing.

Jordi Silvestre-Ryan1, Ian Holmes2.   

Abstract

We develop a general computational approach for improving the accuracy of basecalling with Oxford Nanopore's 1D2 and related sequencing protocols. Our software PoreOver ( https://github.com/jordisr/poreover ) finds the consensus of two neural networks by aligning their probability profiles, and is compatible with multiple nanopore basecallers. When applied to the recently-released Bonito basecaller, our method reduces the median sequencing error by more than half.

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Year:  2021        PMID： 33468205      PMCID： PMC7814537          DOI： 10.1186/s13059-020-02255-1

Source DB:  PubMed          Journal:  Genome Biol        ISSN： 1474-7596            Impact factor:   13.583


  11 in total

1.  Evaluation of Dynamic Time Warp Barycenter Averaging (DBA) for its Potential in Generating a Consensus Nanopore Signal for Genetic and Epigenetic Sequences.

Authors:  Rachel S L Chan; Paul Gordon; Michael R Smith
Journal:  Annu Int Conf IEEE Eng Med Biol Soc       Date:  2018-07

2.  Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.

Authors:  Heng Li
Journal:  Bioinformatics       Date:  2016-03-19       Impact factor: 6.937

3.  DeepNano-blitz: a fast base caller for MinION nanopore sequencers.

Authors:  Vladimír Boža; Peter Perešíni; Broňa Brejová; Tomáš Vinař
Journal:  Bioinformatics       Date:  2020-08-15       Impact factor: 6.937

Review 4.  Three decades of nanopore sequencing.

Authors:  David Deamer; Mark Akeson; Daniel Branton
Journal:  Nat Biotechnol       Date:  2016-05-06       Impact factor: 54.908

5.  Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning.

Authors:  Haotian Teng; Minh Duc Cao; Michael B Hall; Tania Duarte; Sheng Wang; Lachlan J M Coin
Journal:  Gigascience       Date:  2018-05-01       Impact factor: 6.524

6.  A complete bacterial genome assembled de novo using only nanopore sequencing data.

Authors:  Nicholas J Loman; Joshua Quick; Jared T Simpson
Journal:  Nat Methods       Date:  2015-06-15       Impact factor: 28.547

7.  Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.

Authors:  Kishwar Shafin; Trevor Pesout; Ryan Lorig-Roach; Marina Haukness; Hugh E Olsen; Colleen Bosworth; Joel Armstrong; Kristof Tigyi; Nicholas Maurer; Sergey Koren; Fritz J Sedlazeck; Tobias Marschall; Simon Mayes; Vania Costa; Justin M Zook; Kelvin J Liu; Duncan Kilburn; Melanie Sorensen; Katy M Munson; Mitchell R Vollger; Jean Monlong; Erik Garrison; Evan E Eichler; Sofie Salama; David Haussler; Richard E Green; Mark Akeson; Adam Phillippy; Karen H Miga; Paolo Carnevali; Miten Jain; Benedict Paten
Journal:  Nat Biotechnol       Date:  2020-05-04       Impact factor: 54.908

8.  DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads.

Authors:  Vladimír Boža; Broňa Brejová; Tomáš Vinař
Journal:  PLoS One       Date:  2017-06-05       Impact factor: 3.240

9.  Performance of neural network basecalling tools for Oxford Nanopore sequencing.

Authors:  Ryan R Wick; Louise M Judd; Kathryn E Holt
Journal:  Genome Biol       Date:  2019-06-24       Impact factor: 13.583

10.  Fast gap-affine pairwise alignment using the wavefront algorithm.

Authors:  Santiago Marco-Sola; Juan Carlos Moure; Miquel Moreto; Antonio Espinosa
Journal:  Bioinformatics       Date:  2021-05-01       Impact factor: 6.937
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  10 in total

1.  Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies.

Authors:  Alexander S Leonard; Danang Crysnanto; Zih-Hua Fang; Michael P Heaton; Brian L Vander Ley; Carolina Herrera; Heinrich Bollwein; Derek M Bickhart; Kristen L Kuhn; Timothy P L Smith; Benjamin D Rosen; Hubert Pausch
Journal:  Nat Commun       Date:  2022-05-31       Impact factor: 17.694

Review 2.  Nanopore sequencing and its application to the study of microbial communities.

Authors:  Laura Ciuffreda; Héctor Rodríguez-Pérez; Carlos Flores
Journal:  Comput Struct Biotechnol J       Date:  2021-03-07       Impact factor: 7.271

3.  Benchmarking of next and third generation sequencing technologies and their associated algorithms for de novo genome assembly.

Authors:  Marios Gavrielatos; Konstantinos Kyriakidis; Demetrios A Spandidos; Ioannis Michalopoulos
Journal:  Mol Med Rep       Date:  2021-02-04       Impact factor: 2.952

Review 4.  Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era.

Authors:  Shangqian Xie; Amy Wing-Sze Leung; Zhenxian Zheng; Dake Zhang; Chuanle Xiao; Ruibang Luo; Ming Luo; Shoudong Zhang
Journal:  Innovation (Camb)       Date:  2021-08-11

5.  Genomic prediction using low-coverage portable Nanopore sequencing.

Authors:  Harrison J Lamb; Ben J Hayes; Imtiaz A S Randhawa; Loan T Nguyen; Elizabeth M Ross
Journal:  PLoS One       Date:  2021-12-15       Impact factor: 3.240

Review 6.  Uncovering Essential Tremor Genetics: The Promise of Long-Read Sequencing.

Authors:  Luca Marsili; Kevin R Duque; Rachel L Bode; Marcelo A Kauffman; Alberto J Espay
Journal:  Front Neurol       Date:  2022-03-23       Impact factor: 4.003

Review 7.  Nanopore sequencing technology and its application in plant virus diagnostics.

Authors:  Kai Sun; Yi Liu; Xin Zhou; Chuanlin Yin; Pengjun Zhang; Qianqian Yang; Lingfeng Mao; Xuping Shentu; Xiaoping Yu
Journal:  Front Microbiol       Date:  2022-07-25       Impact factor: 6.064

Review 8.  Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing.

Authors:  Yohannis Wondwosen Ahmed; Berhan Ababaw Alemu; Sisay Addisu Bekele; Solomon Tebeje Gizaw; Muluken Fekadie Zerihun; Endriyas Kelta Wabalo; Maria Degef Teklemariam; Tsehayneh Kelemu Mihrete; Endris Yibru Hanurry; Tensae Gebru Amogne; Assaye Desalegne Gebrehiwot; Tamirat Nida Berga; Ebsitu Abate Haile; Dessiet Oma Edo; Bizuwork Derebew Alemu
Journal:  Clin Epigenetics       Date:  2022-08-27       Impact factor: 7.259

9.  Machine Boss: rapid prototyping of bioinformatic automata.

Authors:  Jordi Silvestre-Ryan; Yujie Wang; Mehak Sharma; Stephen Lin; Yolanda Shen; Shihab Dider; Ian Holmes
Journal:  Bioinformatics       Date:  2021-04-09       Impact factor: 6.931

10.  ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone.

Authors:  Amrita Srivathsan; Leshon Lee; Kazutaka Katoh; Emily Hartop; Sujatha Narayanan Kutty; Johnathan Wong; Darren Yeo; Rudolf Meier
Journal:  BMC Biol       Date:  2021-09-29       Impact factor: 7.431
  10 in total

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