ArticleBriefings in bioinformatics2017
Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly.
Article in Briefings in bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Vertical lossless genomic data compression tools for assembled genomes: A systematic literature review.PloS one · 2020Pooled it
- PGIP: a web server for the rapid taxonomic identification of parasite genomes.Parasites & vectors · 2025Article
- Advances in long-read single-cell transcriptomics.Human genetics · 2024Review
- Dynamics of soil microbial communities involved in carbon cycling along three successional forests in southern China.Frontiers in microbiology · 2023Article
- Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales.Frontiers in microbiology · 2020Review
- Athena: Automated Tuning of k-mer based Genomic Error Correction Algorithms using Language Models.Scientific reports · 2019Article
- Alignment-free inference of hierarchical and reticulate phylogenomic relationships.Briefings in bioinformatics · 2019Review
- A Sequence-Based Novel Approach for Quality Evaluation of Third-Generation Sequencing Reads.Genes · 2019Article
- The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly.GigaScience · 2018Article
- Article
- Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution.Nature communications · 2018Article
- Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery.Genome biology · 2018Article
- Gerbil: a fast and memory-efficientAlgorithms for molecular biology : AMB · 2017Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencers such as Illumina can now produce reads up to 300 bp with high throughput, which is attractive for genome assembly. A first step in genome assembly is to computationally correct sequencing errors. However, correcting all errors in these longer reads is challenging. Here, we show that reads with remaining errors after correction often overlap repeats, where short erroneous k-mers occur in other copies of the repeat. We developed an iterative error correction pipeline that runs the previously published String Graph Assembler (SGA) in multiple rounds of k-mer-based correction with an increasing k-mer size, followed by a final round of overlap-based correction. By combining the advantages of small and large k-mers, this approach corrects more errors in repeats and minimizes the total amount of erroneous reads. We show that higher read accuracy increases contig lengths two to three times. We provide SGA-Iteratively Correcting Errors (https://github.com/hillerlab/IterativeErrorCorrection/) that implements iterative error correction by using modules from SGA.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.