ArticleBioinformatics (Oxford, England)2012
SEQuel: improving the accuracy of genome assemblies.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Long-read reconstruction of many diverse haplotypes with devider.Genome research · 2025Article
- Dysgu: efficient structural variant calling using short or long reads.Nucleic acids research · 2022Article
- Buffering updates enables efficient dynamic de Bruijn graphs.Computational and structural biotechnology journal · 2021Article
- Genome skimming and exploration of DNA barcodes for Taiwan endemic cypresses.Scientific reports · 2020Article
- Graph Traversal Edit Distance and Extensions.Journal of computational biology : a journal of computational molecular cell biology · 2020Article
- Comparative analysis of corrected tiger genome provides clues to its neuronal evolution.Scientific reports · 2019Article
- Draft genome sequence data of T-5 likeData in brief · 2019Article
- Mitogenome analysis of dwarf pufferfish (Journal of genetics · 2019Article
- Complete Assembly of the Genome of anFrontiers in microbiology · 2019Article
- Size does matter: Parallel evolution of adaptive thermal tolerance and body size facilitates adaptation to climate change in domestic cattle.Ecology and evolution · 2018Article
- Article
- Conversion of Methionine to Cysteine inFrontiers in microbiology · 2018Article
- GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly.Genome research · 2017Article
- The Antibody Repertoire of Colorectal Cancer.Molecular & cellular proteomics : MCP · 2017Article
- Succinct colored de Bruijn graphs.Bioinformatics (Oxford, England) · 2017Article
- Genome Sequence of "Genome announcements · 2017Article
- Assembly of long error-prone reads using de Bruijn graphs.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Draft Genome Sequence of a Pseudomonas aeruginosa Strain Able To Decompose N,N-Dimethyl Formamide.Genome announcements · 2016Article
- Article
- Draft Genome Sequence of the Fungus Penicillium brasilianum MG11.Genome announcements · 2015Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
motivationAssemblies of next-generation sequencing (NGS) data, although accurate, still contain a substantial number of errors that need to be corrected after the assembly process. We develop SEQuel, a tool that corrects errors (i.e. insertions, deletions and substitution errors) in the assembled contigs. Fundamental to the algorithm behind SEQuel is the positional de Bruijn graph, a graph structure that models k-mers within reads while incorporating the approximate positions of reads into the model.
resultsSEQuel reduced the number of small insertions and deletions in the assemblies of standard multi-cell Escherichia coli data by almost half, and corrected between 30% and 94% of the substitution errors. Further, we show SEQuel is imperative to improving single-cell assembly, which is inherently more challenging due to higher error rates and non-uniform coverage; over half of the small indels, and substitution errors in the single-cell assemblies were corrected. We apply SEQuel to the recently assembled Deltaproteobacterium SAR324 genome, which is the first bacterial genome with a comprehensive single-cell genome assembly, and make over 800 changes (insertions, deletions and substitutions) to refine this assembly. AVAILABILITY: SEQuel can be used as a post-processing step in combination with any NGS assembler and is freely available at http://bix.ucsd.edu/SEQuel/.
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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.