Quake: quality-aware detection and correction of sequencing errors

We introduce Quake, a program to detect and correct errors in DNA sequencing reads. Using a maximum likelihood approach incorporating quality values and nucleotide specific miscall rates, Quake achieves the highest accuracy on realistically simulated reads. We further demonstrate substantial improvements in de novo assembly and SNP detection after using Quake. Quake can be used for any size project, including more than one billion human reads, and is freely available as open source software from http://www.cbcb.umd.edu/software/quake.

• Publication year

  2010

• Venue

  Genome Biology

• Publication date

  2010-11-29

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1186/gb-2010-11-11-r116PMID 21114842PMCID 3156955
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Cancer genomics identifies determinants of tumor biology

  2010cited by this paper
• Hadoop++

  2010cited by this paper
• A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware

  2010cited by this paper
• Model‐Based Quality Assessment and Base‐Calling for Second‐Generation Sequencing Data

  2010cited by this paper
• Reptile: representative tiling for short read error correction

  2010cited by this paper
• De novo assembly of human genomes with massively parallel short read sequencing.

  2010influential reference
• Application of second-generation sequencing to cancer genomics

  2010cited by this paper
• Correction of sequencing errors in a mixed set of reads

  2010cited by this paper
• A comprehensive catalogue of somatic mutations from a human cancer genome

  2010cited by this paper
• Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction

  2010cited by this paper
• Next-generation genomics: an integrative approach

  2010cited by this paper
• Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction

  2009cited by this paper
• SNP detection for massively parallel whole-genome resequencing

  2009cited by this paper
• Accurate determination of microbial diversity from 454 pyrosequencing data

  2009cited by this paper
• The Sequence Alignment/Map format and SAMtools

  2009cited by this paper
• Finding optimal threshold for correction error reads in DNA assembling

  2009cited by this paper
• Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species.

  2009cited by this paper
• BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing.

  2009cited by this paper
• Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction

  2009cited by this paper
• Recount: expectation maximization based error correction tool for next generation sequencing data.

  2009cited by this paper
• De novo fragment assembly with short mate-paired reads: Does the read length matter?

  2009influential reference
• The impact of retrotransposons on human genome evolution

  2009cited by this paper
• How to map billions of short reads onto genomes

  2009cited by this paper
• Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing.

  2009cited by this paper
• The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group.

  2009cited by this paper
• SNP detection for massively parallel whole-genome resequencing.

  2009cited by this paper
• Improved base calling for the Illumina Genome Analyzer using machine learning strategies

  2009cited by this paper
• SHREC: a short-read error correction method

  2009influential reference
• ABySS: a parallel assembler for short read sequence data.

  2009cited by this paper
• Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

  2009influential reference
• 1000 Genomes project

  2008cited by this paper
• Next-generation DNA sequencing

  2008cited by this paper
• Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

  2008influential reference
• ALLPATHS: de novo assembly of whole-genome shotgun microreads.

  2008cited by this paper
• Mapping short DNA sequencing reads and calling variants using mapping quality scores.

  2008cited by this paper
• 1000 Genomes Project

  2008cited by this paper
• MapReduce: simplified data processing on large clusters

  2008cited by this paper
• Alta-Cyclic: a self-optimizing base caller for next-generation sequencing

  2008cited by this paper
• Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

  2008influential reference
• Univariate Discrete Distributions

  2006cited by this paper
• Univariate Discrete Distributions: Johnson/Univariate Discrete Distributions

  2005cited by this paper
• Adjust quality scores from alignment and improve sequencing accuracy.

  2004cited by this paper
• Versatile and open software for comparing large genomes

  2004influential reference
• Automated correction of genome sequence errors.

  2004cited by this paper
• Correcting errors in shotgun sequences.

  2003cited by this paper
• An exponential dispersion model for the distribution of human single nucleotide polymorphisms.

  2003cited by this paper
• ARACHNE: a whole-genome shotgun assembler.

  2002cited by this paper
• An Eulerian path approach to DNA fragment assembly

  2001cited by this paper
• The Elements of Statistical Learning: Data Mining, Inference, and Prediction

  2001cited by this paper
• OpenMP: an industry standard API for shared-memory programming

  1998cited by this paper
• Toward Simplifying and Accurately Formulating Fragment Assembly

  1995cited by this paper
• Univariate Discrete Distributions

  1993cited by this paper
• BMC Bioinformatics BioMed Central Methodology article Probabilistic base calling of Solexa sequencing data

  year unknowncited by this paper

• Phylogenomic analysis of Cervidae provides insights into antler origin and evolution.

  2026cites this paper
• A Reference Assembly for the Legume Cover Crop Smooth Vetch Vicia villosa Roth var. glabrescens

  2026cites this paper
• Genomes of critically endangered saola are shaped by population structure and purging

  2025cites this paper
• Optimizing performance of parallel computing platforms for large-scale genome data analysis

  2025cites this paper
• Frateuria hangzhouensis sp. nov. Isolated from Soil of Moso Bamboo Forest in Hangzhou, China

  2025cites this paper
• Ecological Toxicity, Oxidative Stress and Impacts of Microplastics on Fish Gills

  2025cites this paper
• Comparative genomics of the parasite Trichomonas vaginalis reveals genes involved in spillover from birds to humans

  2025cites this paper
• Yerba mate (Ilex paraguariensis) genome provides new insights into convergent evolution of caffeine biosynthesis

  2025cites this paper
• MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF files

  2025cites this paper
• Integrative multi-omics reveal the regulatory mechanism of golden-thread wood color in Phoebe zhennan.

  2025cites this paper
• Whole genome sequencing and functional annotation of Fusarium oxysporum f. sp. lentis to unravel virulence and secondary metabolite biosynthesis gene clusters

  2025cites this paper
• An Asynchronous Distributed-Memory Parallel Algorithm for $k$-Mer Counting

  2025cites this paper
• K-mer-based Approaches to Bridging Pangenomics and Population Genetics

  2025cites this paper
• Machine learning-based prediction of proteins’ architecture using sequences of amino acids and structural alphabets

  2024cites this paper
• Utilization of whey-based growth media for production of recombinant papain-like protease of SARS- CoV-2 under Escherichia coli host cells

  2024cites this paper
• Comparative genomics of the sexually transmitted parasite Trichomonas vaginalis reveals relaxed and convergent evolution and genes involved in spillover from birds to humans

  2024cites this paper
• Integrative and conjugative elements of Pasteurella multocida: Prevalence and signatures in population evolution

  2024cites this paper
• Emergence of a novel multi-resistance-mediating integrative and conjugative element ICEPmu3 in Pasteurella multocida 1

  2024cites this paper
• Enrichment of novel entomopathogenic Pseudomonas species enhances willow resistance to leaf beetles

  2024cites this paper
• Yerba mate (Ilex paraguariensis) genome provides new insights into convergent evolution of caffeine biosynthesis

  2024cites this paper
• Space-efficient computation of k-mer dictionaries for large values of k

  2024cites this paper
• MAFcounter: An efficient tool for counting the occurrences of k-mers in MAF files

  2024cites this paper
• First draft of the nuclear genome assembly and annotation of the multi-stress tolerant desert giant milkweed Calotropis procera

  2024cites this paper
• BigDEC: A multi-algorithm Big Data tool based on the k-mer spectrum method for scalable short-read error correction

  2024cites this paper
• TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing

  2024cites this paper
• Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure

  2024cites this paper
• Illumina reads correction: evaluation and improvements

  2024cites this paper
• A high-precision genome size estimator based on the k-mer histogram correction

  2024cites this paper
• Functional activity of endophytic bacteria G9H01 with high salt tolerance and anti-Magnaporthe oryzae that isolated from saline-alkali-tolerant rice.

  2024cites this paper
• A Novel Approach for Accurate Sequence Assembly Using de Bruijn graphs

  2024cites this paper
• k-mer-based approaches to bridging pangenomics and population genetics

  2024cites this paper
• The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome

  2023cites this paper
• K-Mer-Based Genome Size Estimation in Theory and Practice.

  2023cites this paper
• Mutational profile of the regenerative process and de novo genome assembly of the planarian Schmidtea polychroa

  2023cites this paper
• De novo assembly of the black flounder genome. Why do pleuronectiformes have such a small genome size?

  2023cites this paper
• A primer-independent DNA polymerase-based method for competent whole-genome amplification of intermediate to high GC sequences

  2023cites this paper
• EVALUATING TRANSCRIPTOME ASSEMBLY POTENTIAL BY DIFFERENT DE NOVO SEQUENCE ASSEMBLER TYPES

  2023cites this paper
• Methods to improve the accuracy of next-generation sequencing

  2023cites this paper
• A primer-independent DNA polymerase-based method for competent whole-genome amplification of intermediate to high GC sequences

  2023cites this paper
• A phylogenomic analysis of Limosilactobacillus reuteri reveals ancient and stable evolutionary relationships with rodents and birds and zoonotic transmission to humans

  2023cites this paper
• JASPER: A fast genome polishing tool that improves accuracy of genome assemblies

  2023cites this paper
• A draft Diabrotica virgifera virgifera genome: insights into control and host plant adaption by a major maize pest insect

  2023cites this paper
• Genomic insight into the insecticidal potential of a new Pseudomonas chlororaphis isolate.

  2023cites this paper
• Salipaludibacillus daqingensis sp. nov., a moderately halophilic bacterium isolated from an oilfield.

  2023cites this paper
• Genome sequence assembly algorithms and misassembly identification methods

  2022cites this paper
• Going From Molecules to Genomic Variations to Scientific Discovery: Intelligent Algorithms and Architectures for Intelligent Genome Analysis

  2022cites this paper
• The complete mitochondrial genome of giant cricket, Tarbinskiellus portentosus (Orthoptera: Gryllidae) and its curation

  2022cites this paper
• From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures

  2022cites this paper
• Alteribacter keqinensis sp. nov., a moderately halophilic bacterium isolated from a soda lake.

  2022cites this paper
• Genome Sequencing of Hericium coralloides by a Combination of PacBio RS II and Next-Generation Sequencing Platforms

  2022cites this paper
• Unveiling lignocellulolytic trait of a goat omasum inhabitant Klebsiella variicola strain HSTU-AAM51 in light of biochemical and genome analyses

  2022cites this paper
• Accurate k-mer Classification Using Read Profiles

  2022cites this paper
• Massilia phyllostachyos sp. nov., Isolated from the Roots of Moso Bamboo in China

  2022cites this paper
• The Science and Art of Clinical Genetic Variant Classification and Its Impact on Test Accuracy.

  2021cites this paper
• Enabling Genomics Pipelines in Commodity Personal Computers With Flash Storage

  2021cites this paper
• Genome assembly of the roundjaw bonefish (Albula glossodonta), a vulnerable circumtropical sportfish

  2021cites this paper
• SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing

  2021cites this paper
• Evaluating whole-genome sequencing quality metrics for enteric pathogen outbreaks

  2021cites this paper
• The Aphelenchus avenae genome highlights evolutionary adaptation to desiccation

  2021cites this paper
• Frigate: a fast, in-memory tool for counting and querying k-mers

  2021cites this paper
• Probabilistic Models of k-mer Frequencies (Extended Abstract)

  2021cites this paper
• Shiga Toxin-Producing Escherichia coli (STEC) and STEC-Associated Virulence Genes in Raw Ground Pork in Canada.

  2021cites this paper
• QTL mapping for Fusarium wilt resistance based on the whole-genome resequencing and their association with functional genes in Raphanus sativus

  2021cites this paper
• Genomic, Antimicrobial, and Aphicidal Traits of Bacillus velezensis ATR2, and Its Biocontrol Potential against Ginger Rhizome Rot Disease Caused by Bacillus pumilus

  2021cites this paper
• Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions

  2021cites this paper
• Genome Sequence Analysis of the Oleaginous Yeast, Rhodotorula diobovata, and Comparison of the Carotenogenic and Oleaginous Pathway Genes and Gene Products with Other Oleaginous Yeasts

  2021cites this paper
• First insight into the whole genome shotgun sequence of the endangered noble pen shell Pinna nobilis: a giant bivalve undergoing a mass mortality event

  2021cites this paper
• SPRISS: approximating frequent k-mers by sampling reads, and applications

  2021cites this paper
• The genomic basis of evolutionary differentiation among honey bees

  2021influential citation
• Whole-genome sequence of Diaporthe citri isolate NFHF-8-4, the causal agent of citrus melanose.

  2021cites this paper
• Comprehensive Evaluation of Error-Correction Methodologies for Genome Sequencing Data

  2021cites this paper
• Figbird: A probabilistic method for filling gaps in genome assemblies

  2021cites this paper
• Characterization of the extracellular fructanase FruA in Lactobacillus crispatus and its contribution to fructan hydrolysis in breadmaking.

  2020cites this paper
• Draft Genome Sequence of Alkalicoccus halolimnae BZ-SZ-XJ29T, a Moderately Halophilic Bacterium Isolated from a Salt Lake

  2020cites this paper
• CHTKC: a robust and efficient k-mer counting algorithm based on a lock-free chaining hash table

  2020cites this paper
• Genomics of Atlantic Forest Mycobacteriaceae strains unravels a mobilome diversity with a novel integrative conjugative element and plasmids harbouring T7SS

  2020cites this paper
• Comprehensive assessment of error correction methods for high-throughput sequencing data.

  2020cites this paper
• Citrus Genomes: From Sequence Variations to Epigenetic Modifications

  2020cites this paper
• Long-read error correction: a survey and qualitative comparison

  2020cites this paper
• Mimicry diversification in Papilio dardanus via a genomic inversion in the regulatory region of engrailed–invected

  2020cites this paper
• Quantitative comparison of within-sample heterogeneity scores for DNA methylation data

  2020cites this paper
• VA-Store: A Virtual Approximate Store Approach to Supporting Repetitive Big Data in Genome Sequence Analyses

  2020influential citation
• Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata

  2020cites this paper
• SMusket: Spark-based DNA error correction on distributed-memory systems

  2020cites this paper
• Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling

  2020cites this paper
• Read trimming has minimal effect on bacterial SNP-calling accuracy

  2020cites this paper
• GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes

  2020cites this paper
• Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields

  2020influential citation
• A Classification of de Bruijn Graph Approaches for De Novo Fragment Assembly

  2020cites this paper
• Improving de novo Assembly Based on Read Classification

  2020cites this paper
• Clover: a clustering-oriented de novo assembler for Illumina sequences

  2020cites this paper
• LJA: Assembling Long and Accurate Reads Using Multiplex de Bruijn Graphs

  2020cites this paper
• Multiomics Study of Gut Bacteria and Host Metabolism in Irritable Bowel Syndrome and Depression Patients

  2020cites this paper
• Extraction of Long k-mers Using Spaced Seeds

  2020cites this paper
• Methods for De-novo Genome Assembly

  2020cites this paper
• RepAHR: an improved approach for de novo repeat identification by assembly of the high-frequency reads

  2020cites this paper
• An Efficient Trimming Algorithm based on Multi-Feature Fusion Scoring Model for NGS Data

  2020cites this paper
• Deep Neural Network: An Efficient and Optimized Machine Learning Paradigm for Reducing Genome Sequencing Error

  2020cites this paper
• The meadow jumping mouse genome and transcriptome suggest mechanisms of hibernation

  2020cites this paper
• Fast Approximation of Frequent k-Mers and Applications to Metagenomics

  2019cites this paper