ArticleGenome research2016
Improved assembly of noisy long reads by k-mer validation.
Article in Genome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- MinION Sequencing of colorectal cancer tumour microbiomes-A comparison with amplicon-based and RNA-Sequencing.PloS one · 2020Trial
- Efficient De Novo Assembly and Recovery of Microbial Genomes from Complex Metagenomes Using a Reduced Set of k-mers.Interdisciplinary sciences, computational life sciences · 2026Article
- Strong bias in long-read sequencing prevents assembly ofGenome research · 2026Article
- Flow Cytometry and K-mer-Based Approach for Genome Size Estimation of Clusterbean: A Case Study.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- Constructing telomere-to-telomere diploid genome by polishing haploid nanopore-based assembly.Nature methods · 2024Article
- Evaluating supervised and unsupervised background noise correction in human gut microbiome data.PLoS computational biology · 2022Article
- First genomic insights into theFrontiers in plant science · 2022Article
- Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies.International journal of molecular sciences · 2021Review
- Intrinsic laws of k-mer spectra of genome sequences and evolution mechanism of genomes.BMC evolutionary biology · 2020Article
- A Mini-review of the Computational Methods Used in Identifying RNA 5-Methylcytosine Sites.Current genomics · 2020Review
- Article
- Hierarchical Clustering of DNA k-mer Counts in RNAseq Fastq Files Identifies Sample Heterogeneities.International journal of molecular sciences · 2018Article
- Article
- HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning.Scientific reports · 2018Article
- A recurrence-based approach for validating structural variation using long-read sequencing technology.GigaScience · 2017Article
- deBGR: an efficient and near-exact representation of the weighted de Bruijn graph.Bioinformatics (Oxford, England) · 2017Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome assembly depends critically on read length. Two recent technologies, from Pacific Biosciences (PacBio) and Oxford Nanopore, produce read lengths >20 kb, which yield de novo genome assemblies with vastly greater contiguity than those based on Sanger, Illumina, or other technologies. However, the very high error rates of these two new technologies (∼15% per base) makes assembly imprecise at repeats longer than the read length and computationally expensive. Here we show that the contiguity and quality of the assembly of these noisy long reads can be significantly improved at a minimal cost, by leveraging on the low error rate and low cost of Illumina short reads. Namely, k-mers from the PacBio raw reads that are not present in Illumina reads (which account for ∼95% of the distinct k-mers) are deemed sequencing errors and ignored at the seed alignment step. By focusing on the ∼5% of k-mers that are error free, read overlap sensitivity is dramatically increased. Of equal importance, the validation procedure can be extended to exclude repetitive k-mers, which prevents read miscorrection at repeats and further improves the resulting assemblies. We tested the k-mer validation procedure using one long-read technology (PacBio) and one assembler (MHAP/Celera Assembler), but it is very likely to yield analogous improvements with alternative long-read technologies and assemblers, such as Oxford Nanopore and BLASR/DALIGNER/Falcon, respectively.
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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.