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GemSIM: general, error-model based simulator of next-generation sequencing data

Kerensa E McElroy, Fabio Luciani, Torsten Thomas
2012 BMC Genomics  
Conclusions: Next-generation sequencing has unprecedented potential for assessing genetic diversity, however analysis is complicated as error profiles can vary noticeably even between different runs of  ...  GemSIM creates and uses empirically derived, sequence-context based error models to realistically emulate individual sequencing runs and/or technologies.  ...  Error analysis Error models for Illumina v4, Illumina v5, and Roche/ 454 were analysed with GemStats. Error rates are summarised in Table 3 .  ... 
doi:10.1186/1471-2164-13-74 pmid:22336055 pmcid:PMC3305602 fatcat:27efclimebcpdgzj5luevoqv6m

Sequencing error profiles of Illumina sequencing instruments

Nicholas Stoler, Anton Nekrutenko
2021 NAR Genomics and Bioinformatics  
Here, we developed a method able to retroactively determine the error rate of most public sequencing datasets.  ...  We show the importance of sequence context, especially the phenomenon where preceding bases bias the following bases toward the same identity.  ...  We would like to thank the entire Galaxy team for supporting this effort. Conflict of interest statement. None declared.  ... 
doi:10.1093/nargab/lqab019 pmid:33817639 pmcid:PMC8002175 fatcat:dz7zcfymbvggba337byie7zfke

A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE

Kevin P. Keegan, William L. Trimble, Jared Wilkening, Andreas Wilke, Travis Harrison, Mark D'Souza, Folker Meyer, Scott Markel
2012 PLoS Computational Biology  
For shotgun metagenomic data, we believe that DRISEE provides estimates of sequencing error that are more accurate and less constrained by technical limitations than existing methods that rely on reference  ...  data from the 454 and Illumina sequencing platforms.  ...  Salazar for comments on the manuscript, as well as Elizabeth M. Glass and the MG-RAST development team for technical support. Author Contributions  ... 
doi:10.1371/journal.pcbi.1002541 pmid:22685393 pmcid:PMC3369934 fatcat:b4fvqzj2bna6zljh37fwarr2yq

Pseudoalignment facilitates assignment of error-prone Ultima Genomics reads [article]

A. Sina Booeshaghi, Lior Pachter
2022 bioRxiv   pre-print
To compensate for these errors, we explore the use of pseudoalignment for read assignment, and find that it can perform better than standard read alignment.  ...  We analyze single-cell RNA-seq data sequenced with Ultima Genomics technology and find high error rates in and near homopolymers.  ...  For context, liquid biopsies can benefit from accurate sequencing of 1 error per 10 million bases (Higgins et al. 2019) , and the accuracy of Ultima Genomics for TMSB4X is worse than 80,000 indels per  ... 
doi:10.1101/2022.06.04.494845 fatcat:4wjmacicjzdnblcfzs3ibyo2za

Discovering motifs that induce sequencing errors

Manuel Allhoff, Alexander Schönhuth, Marcel Martin, Ivan G Costa, Sven Rahmann, Tobias Marschall
2013 BMC Bioinformatics  
We apply our method to several datasets from Illumina GA IIx, HiSeq 2000, and MiSeq sequencers. We confirm previously known error-causing sequence contexts and report new more specific ones.  ...  Results: Here, for the first time, we describe a statistically rigorous framework for the discovery of motifs that induce sequencing errors.  ...  In this study, we focus on a class of such errors that are characteristic for Illumina sequencing platforms [5] .  ... 
doi:10.1186/1471-2105-14-s5-s1 pmid:23735080 pmcid:PMC3622629 fatcat:elt35x6zh5htzbwbvk6xgkaii4

An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome

Marco Ferrarini, Marco Moretto, Judson A Ward, Nada Šurbanovski, Vladimir Stevanović, Lara Giongo, Roberto Viola, Duccio Cavalieri, Riccardo Velasco, Alessandro Cestaro, Daniel J Sargent
2013 BMC Genomics  
The results we present suggest PacBio data will be of immense utility for the development of genome sequence assemblies containing fewer unresolved gaps and ambiguities and a significantly smaller number  ...  Results: Following error-correction, a total of 28,638 PacBio RS reads were recovered with a mean read length of 1,902 bp totalling 54,492,250 nucleotides and representing an average depth of coverage  ...  Acknowledgements This work was funded by a grant to Fondazione Edmund Mach by the Autonomous Province of Trento (Italy).  ... 
doi:10.1186/1471-2164-14-670 pmid:24083400 pmcid:PMC3853357 fatcat:4pq2crlxqvgbzo4bocciwzsyba

Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis

Jason L Weirather, Mariateresa de Cesare, Yunhao Wang, Paolo Piazza, Vittorio Sebastiano, Xiu-Jie Wang, David Buck, Kin Fai Au
2017 F1000Research  
Both PacBio and ONT Conclusions: sequencing are suitable for full-length single-molecule transcriptome analysis.  ...  As this first use of ONT reads in a Hybrid-Seq analysis has shown, both PacBio and ONT can benefit from a combined Illumina strategy.  ...  Strengths: 1) The demonstration of the dependence of sequencing quality (or the Fraction of read aligned) on read length (figure 2) both for single pass reads (subreads for PacBio and 1D for ONT) and for  ... 
doi:10.12688/f1000research.10571.1 pmid:28868132 pmcid:PMC5553090 fatcat:f5aw4cksrbeblif45yfesqr42e

High-Throughput, Amplicon-Based Sequencing of the CREBBP Gene as a Tool to Develop a Universal Platform-Independent Assay

Marc W. Fuellgrabe, Dietrich Herrmann, Henrik Knecht, Sven Kuenzel, Michael Kneba, Christiane Pott, Monika Brüggemann, Ramy K. Aziz
2015 PLoS ONE  
to the result of sequence analysis from the remaining platforms.  ...  Additionally, bioinformatic methods are described to determine platform dependent errors.  ...  The authors thank the Interlaboratory Robustness of Next-generation sequencing (IRON) Phase II Study Group members for helpful discussions on the CREBBP assay development. Author Contributions  ... 
doi:10.1371/journal.pone.0129195 pmid:26057250 pmcid:PMC4461278 fatcat:tsprtezgkjfwhdniz3lbnupvqa

Overview of single-molecule long RNA-seq reads and their transcriptomic applications in plant research

Kan Liu
2018 Journal of Plant Biology and Crop Research  
Nowadays, alternative splicing and gene-fusion analysis can take advantage of the third-generation sequencing technology such as PacBio ISO-Seq and Oxford Nanopore Technologies (ONT) MinION RNA-Seq [1]  ...  Overview of single-molecule long RNA-seq reads and their transcriptomic applications in plant research. J Plant Biol Crop Res. 2018; 1(1): 1004.  ...  Short read sequencing using the Illumina platform to evaluate and correct the error of long reads is both necessary and powerful in the further transcriptome analysis [4] .  ... 
doi:10.33582/2637-7721/1004 fatcat:34ssesixr5cl7d46n7ir7sulou

MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing

Hardik I. Parikh, Vishal N. Koparde, Steven P. Bradley, Gregory A. Buck, Nihar U. Sheth
2016 BMC Bioinformatics  
For this analysis on the Illumina platform, merging and quality filtering of paired-end reads are essential first steps in data analysis to ensure the accuracy and reliability of downstream analysis.  ...  Recent advances in next-generation sequencing have revolutionized genomic research. 16S rRNA amplicon sequencing using paired-end sequencing on the MiSeq platform from Illumina, Inc., is being used to  ...  We especially thank K Hendricks-Munoz and P Xu for providing the datasets for development and testing purposes.  ... 
doi:10.1186/s12859-016-1358-1 pmid:27905885 pmcid:PMC5134250 fatcat:qrsocgl5jfg2zk65osmv4bujrm

Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis

Jason L Weirather, Mariateresa de Cesare, Yunhao Wang, Paolo Piazza, Vittorio Sebastiano, Xiu-Jie Wang, David Buck, Kin Fai Au
2017 F1000Research  
Both PacBio and ONT sequencing are suitable for Conclusions: full-length single-molecule transcriptome analysis.  ...  As this first use of ONT reads in a Hybrid-Seq analysis has shown, both PacBio and ONT can benefit from a combined Illumina strategy.  ...  ., Research Scientist at the University of Iowa Carver College of Medicine, for critical reading of the manuscript.  ... 
doi:10.12688/f1000research.10571.2 pmid:28868132 pmcid:PMC5553090 fatcat:6ajqnt4gybaa3dwmg2hsastlw4

Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence

Claire T. Deakin, Jeffrey J. Deakin, Samantha L. Ginn, Paul Young, David Humphreys, Catherine M. Suter, Ian E. Alexander, Claus V. Hallwirth
2014 Nucleic Acids Research  
Such errors, which potentially impact barcoding studies in an application-dependent manner, are consistent with the existence of both stochastic and systematic error, the mechanism of which is yet to be  ...  Analysis of clones marked with barcoded vectors requires accurate identification of potentially large numbers of individually rare barcodes, when the exact number, sequence identity and abundance are unknown  ...  ACKNOWLEDGEMENT We thank Margot Latham (The Children's Hospital at Westmead) for assistance in manuscript preparation.  ... 
doi:10.1093/nar/gku607 pmid:25013183 pmcid:PMC4176369 fatcat:zammu4uqmrh5xj4g3igamynfua

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

Maura Costello, Trevor J. Pugh, Timothy J. Fennell, Chip Stewart, Lee Lichtenstein, James C. Meldrim, Jennifer L. Fostel, Dennis C. Friedrich, Danielle Perrin, Danielle Dionne, Sharon Kim, Stacey B. Gabriel (+3 others)
2013 Nucleic Acids Research  
Although error rates for sequencing and polymerase chain reaction (PCR) are well documented, the effects that DNA extraction and other library preparation steps could have on downstream sequence integrity  ...  As researchers begin probing deep coverage sequencing data for increasingly rare mutations and subclonal events, the fidelity of next generation sequencing (NGS) laboratory methods will become increasingly  ...  From MIT's Department of Biological Engineering, the authors thank Professor Peter Dedon for invaluable advice regarding DNA oxidation.  ... 
doi:10.1093/nar/gks1443 pmid:23303777 pmcid:PMC3616734 fatcat:or53w4xsanf5vnfca3gvlrdew4

Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing

Justin M. Zook, Daniel Samarov, Jennifer McDaniel, Shurjo K. Sen, Marc Salit, Janet Kelso
2012 PLoS ONE  
Most algorithms proposed for correction of SSEs require a data set used to calculate association of SSEs with various features in the reads and sequence context.  ...  While the importance of random sequencing errors decreases at higher DNA or RNA sequencing depths, systematic sequencing errors (SSEs) dominate at high sequencing depths and can be difficult to distinguish  ...  Acknowledgments We thank Leslie Biesecker for a careful reading of this manuscript and providing the RNA samples from the ClinSeq Project.  ... 
doi:10.1371/journal.pone.0041356 pmid:22859977 pmcid:PMC3409179 fatcat:rfwkgqvf25effinal4v7uwnlki

HELLO: A hybrid variant calling approach [article]

Anand Ramachandran, Steven S. Lumetta, Eric Klee, Deming Chen
2020 bioRxiv   pre-print
However, these reads have context-dependent indel errors in low-complexity regions, resulting in lower accuracy of small indel calls compared to NGS reads.  ...  AbstractNext Generation Sequencing (NGS) technologies that cost-effectively characterize genomic regions and identify sequence variations using short reads are the current standard for genome sequencing  ...  Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.  ... 
doi:10.1101/2020.03.23.004473 fatcat:4r4ol7z67famjnuwztdizj5mg4
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