ArticleGenome research2011
ECHO: a reference-free short-read error correction algorithm.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Prior knowledge on context-driven DNA fragmentation probabilities can improve de novo genome assembly algorithms.BMC bioinformatics · 2025Article
- How error correction affects polymerase chain reaction deduplication: A survey based on unique molecular identifier datasets of short reads.Quantitative biology (Beijing, China) · 2025Review
- MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads.BMC bioinformatics · 2024Article
- Methods to improve the accuracy of next-generation sequencing.Frontiers in bioengineering and biotechnology · 2023Review
- Genome sequence assembly algorithms and misassembly identification methods.Molecular biology reports · 2022Review
- CARE 2.0: reducing false-positive sequencing error corrections using machine learning.BMC bioinformatics · 2022Article
- Lerna: transformer architectures for configuring error correction tools for short- and long-read genome sequencing.BMC bioinformatics · 2022Article
- Lightweight Pattern Matching Method for DNA Sequencing in Internet of Medical Things.Computational intelligence and neuroscience · 2022Article
- Aberration-corrected ultrafine analysis of miRNA reads at single-base resolution: a k-mer lattice approach.Nucleic acids research · 2021Article
- A hybrid and scalable error correction algorithm for indel and substitution errors of long reads.BMC genomics · 2019Article
- Athena: Automated Tuning of k-mer based Genomic Error Correction Algorithms using Language Models.Scientific reports · 2019Article
- GASAL2: a GPU accelerated sequence alignment library for high-throughput NGS data.BMC bioinformatics · 2019Article
- Deep sequencing of 2009 influenza A/H1N1 virus isolated from volunteer human challenge study participants and natural infections.Virology · 2019Article
- GAAP: A Genome Assembly + Annotation Pipeline.BioMed research international · 2019Article
- Mining statistically-solid k-mers for accurate NGS error correction.BMC genomics · 2018Article
- Article
- Red Clover (Frontiers in plant science · 2018Article
- An efficient error correction algorithm using FM-index.BMC bioinformatics · 2017Article
- Review
- Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly.Briefings in bioinformatics · 2017Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Developing accurate, scalable algorithms to improve data quality is an important computational challenge associated with recent advances in high-throughput sequencing technology. In this study, a novel error-correction algorithm, called ECHO, is introduced for correcting base-call errors in short-reads, without the need of a reference genome. Unlike most previous methods, ECHO does not require the user to specify parameters of which optimal values are typically unknown a priori. ECHO automatically sets the parameters in the assumed model and estimates error characteristics specific to each sequencing run, while maintaining a running time that is within the range of practical use. ECHO is based on a probabilistic model and is able to assign a quality score to each corrected base. Furthermore, it explicitly models heterozygosity in diploid genomes and provides a reference-free method for detecting bases that originated from heterozygous sites. On both real and simulated data, ECHO is able to improve the accuracy of previous error-correction methods by several folds to an order of magnitude, depending on the sequence coverage depth and the position in the read. The improvement is most pronounced toward the end of the read, where previous methods become noticeably less effective. Using a whole-genome yeast data set, it is demonstrated here that ECHO is capable of coping with nonuniform coverage. Also, it is shown that using ECHO to perform error correction as a preprocessing step considerably facilitates de novo assembly, particularly in the case of low-to-moderate sequence coverage depth.
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