Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction
Published 2015 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction
Authors
Keywords
-
Journal
BRIEFINGS IN BIOINFORMATICS
Volume 17, Issue 1, Pages 154-179
Publisher
Oxford University Press (OUP)
Online
2015-05-31
DOI
10.1093/bib/bbv029
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly
- (2015) Sergey Koren et al. CURRENT OPINION IN MICROBIOLOGY
- Improved data analysis for the MinION nanopore sequencer
- (2015) Miten Jain et al. NATURE METHODS
- Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform
- (2015) Melanie Schirmer et al. NUCLEIC ACIDS RESEARCH
- Blue: correcting sequencing errors using consensus and context
- (2014) Paul Greenfield et al. BIOINFORMATICS
- Trowel: a fast and accurate error correction module for Illumina sequencing reads
- (2014) Eun-Cheon Lim et al. BIOINFORMATICS
- Fiona: a parallel and automatic strategy for read error correction
- (2014) Marcel H. Schulz et al. BIOINFORMATICS
- BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads
- (2014) Yun Heo et al. BIOINFORMATICS
- LoRDEC: accurate and efficient long read error correction
- (2014) Leena Salmela et al. BIOINFORMATICS
- proovread : large-scale high-accuracy PacBio correction through iterative short read consensus
- (2014) Thomas Hackl et al. BIOINFORMATICS
- GATB: Genome Assembly & Analysis Tool Box
- (2014) Erwan Drezen et al. BIOINFORMATICS
- HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data
- (2014) Adrianto Wirawan et al. BMC BIOINFORMATICS
- Correcting Illumina data
- (2014) Michael Molnar et al. BRIEFINGS IN BIOINFORMATICS
- MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island
- (2014) Philip M Ashton et al. NATURE BIOTECHNOLOGY
- Correction of sequence-dependent ambiguous bases (Ns) from the 454 pyrosequencing system
- (2014) Sunguk Shin et al. NUCLEIC ACIDS RESEARCH
- A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer
- (2014) Joshua Quick et al. GigaScience
- RACER: Rapid and accurate correction of errors in reads
- (2013) Lucian Ilie et al. BIOINFORMATICS
- Informed and automated k-mer size selection for genome assembly
- (2013) R. Chikhi et al. BIOINFORMATICS
- Sequencing error correction without a reference genome
- (2013) Julie A Sleep et al. BMC BIOINFORMATICS
- An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome
- (2013) Marco Ferrarini et al. BMC GENOMICS
- BayesHammer: Bayesian clustering for error correction in single-cell sequencing
- (2013) Sergey I Nikolenko et al. BMC GENOMICS
- Probabilistic model based error correction in a set of various mutant sequences analyzed by next-generation sequencing
- (2013) Takuyo Aita et al. COMPUTATIONAL BIOLOGY AND CHEMISTRY
- A glimpse into past, present, and future DNA sequencing
- (2013) Marcos Morey et al. MOLECULAR GENETICS AND METABOLISM
- Updating benchtop sequencing performance comparison
- (2013) Sebastian Jünemann et al. NATURE BIOTECHNOLOGY
- Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
- (2013) Chen-Shan Chin et al. NATURE METHODS
- Probabilistic error correction for RNA sequencing
- (2013) Hai-Son Le et al. NUCLEIC ACIDS RESEARCH
- Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data
- (2013) Lauren M. Bragg et al. PLoS Computational Biology
- Reducing assembly complexity of microbial genomes with single-molecule sequencing
- (2013) Sergey Koren et al. GENOME BIOLOGY
- Characterizing and measuring bias in sequence data
- (2013) Michael G Ross et al. GENOME BIOLOGY
- PBSIM: PacBio reads simulator—toward accurate genome assembly
- (2012) Yukiteru Ono et al. BIOINFORMATICS
- Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly
- (2012) H. Li BIOINFORMATICS
- Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data
- (2012) Yongchao Liu et al. BIOINFORMATICS
- Efficient error correction for next-generation sequencing of viral amplicons
- (2012) Pavel Skums et al. BMC BIOINFORMATICS
- A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers
- (2012) Michael Quail et al. BMC GENOMICS
- A survey of error-correction methods for next-generation sequencing
- (2012) X. Yang et al. BRIEFINGS IN BIOINFORMATICS
- Progress in Ion Torrent semiconductor chip based sequencing
- (2012) Barry Merriman et al. ELECTROPHORESIS
- Performance comparison of benchtop high-throughput sequencing platforms
- (2012) Nicholas J Loman et al. NATURE BIOTECHNOLOGY
- Hybrid error correction and de novo assembly of single-molecule sequencing reads
- (2012) Sergey Koren et al. NATURE BIOTECHNOLOGY
- A hybrid approach for the automated finishing of bacterial genomes
- (2012) Ali Bashir et al. NATURE BIOTECHNOLOGY
- Fast, accurate error-correction of amplicon pyrosequences using Acacia
- (2012) Lauren Bragg et al. NATURE METHODS
- Improving PacBio Long Read Accuracy by Short Read Alignment
- (2012) Kin Fai Au et al. PLoS One
- SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
- (2012) Ruibang Luo et al. GigaScience
- Correcting errors in short reads by multiple alignments
- (2011) L. Salmela et al. BIOINFORMATICS
- Error correction of high-throughput sequencing datasets with non-uniform coverage
- (2011) P. Medvedev et al. BIOINFORMATICS
- DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI
- (2011) Yongchao Liu et al. BMC BIOINFORMATICS
- Repeat-aware modeling and correction of short read errors
- (2011) Xiao Yang et al. BMC BIOINFORMATICS
- ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data
- (2011) Osvaldo Zagordi et al. BMC BIOINFORMATICS
- Identification and correction of systematic error in high-throughput sequence data
- (2011) Frazer Meacham et al. BMC BIOINFORMATICS
- Removing Noise From Pyrosequenced Amplicons
- (2011) Christopher Quince et al. BMC BIOINFORMATICS
- Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing
- (2011) André Gilles et al. BMC GENOMICS
- ECHO: A reference-free short-read error correction algorithm
- (2011) W.-C. Kao et al. GENOME RESEARCH
- Efficient de novo assembly of large genomes using compressed data structures
- (2011) J. T. Simpson et al. GENOME RESEARCH
- An integrated semiconductor device enabling non-optical genome sequencing
- (2011) Jonathan M. Rothberg et al. NATURE
- Sequence-specific error profile of Illumina sequencers
- (2011) Kensuke Nakamura et al. NUCLEIC ACIDS RESEARCH
- Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing
- (2011) Sebastian Jaenicke et al. PLoS One
- Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems
- (2011) André E Minoche et al. GENOME BIOLOGY
- HiTEC: accurate error correction in high-throughput sequencing data
- (2010) L. Ilie et al. BIOINFORMATICS
- Correction of sequencing errors in a mixed set of reads
- (2010) L. Salmela BIOINFORMATICS
- Characteristics of 454 pyrosequencing data--enabling realistic simulation with flowsim
- (2010) S. Balzer et al. BIOINFORMATICS
- Reptile: representative tiling for short read error correction
- (2010) X. Yang et al. BIOINFORMATICS
- The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
- (2010) A. McKenna et al. GENOME RESEARCH
- A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware
- (2010) Haixiang Shi et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction
- (2010) Osvaldo Zagordi et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- EDAR: An Efficient Error Detection and Removal Algorithm for Next Generation Sequencing Data
- (2010) Xiaohong Zhao et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions
- (2010) Jens Reeder et al. NATURE METHODS
- A flexible and efficient template format for circular consensus sequencing and SNP detection
- (2010) K. J. Travers et al. NUCLEIC ACIDS RESEARCH
- Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies
- (2010) Osvaldo Zagordi et al. NUCLEIC ACIDS RESEARCH
- High-quality draft assemblies of mammalian genomes from massively parallel sequence data
- (2010) S. Gnerre et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Phenotypic connections in surprising places
- (2010) Bolan Linghu et al. GENOME BIOLOGY
- SHREC: a short-read error correction method
- (2009) J. Schroder et al. BIOINFORMATICS
- Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing
- (2009) W. Qu et al. GENOME RESEARCH
- De novo assembly of human genomes with massively parallel short read sequencing
- (2009) R. Li et al. GENOME RESEARCH
- Accurate determination of microbial diversity from 454 pyrosequencing data
- (2009) Christopher Quince et al. NATURE METHODS
- Continuous base identification for single-molecule nanopore DNA sequencing
- (2009) James Clarke et al. Nature Nanotechnology
- Sequencing technologies — the next generation
- (2009) Michael L. Metzker NATURE REVIEWS GENETICS
- Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays
- (2009) R. Drmanac et al. SCIENCE
- Aggressive assembly of pyrosequencing reads with mates
- (2008) Jason R. Miller et al. BIOINFORMATICS
- SeqAn An efficient, generic C++ library for sequence analysis
- (2008) Andreas Döring et al. BMC BIOINFORMATICS
- De novo fragment assembly with short mate-paired reads: Does the read length matter?
- (2008) M. J. Chaisson et al. GENOME RESEARCH
- ALLPATHS: De novo assembly of whole-genome shotgun microreads
- (2008) J. Butler et al. GENOME RESEARCH
- Accurate whole human genome sequencing using reversible terminator chemistry
- (2008) David R. Bentley et al. NATURE
- Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
- (2008) J. C. Dohm et al. NUCLEIC ACIDS RESEARCH
- Real-Time DNA Sequencing from Single Polymerase Molecules
- (2008) J. Eid et al. SCIENCE
- Short read fragment assembly of bacterial genomes
- (2007) M. J. Chaisson et al. GENOME RESEARCH
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started