ArticleBMC genomics2013
Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF files.BMC bioinformatics · 2025Article
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- Early Detection of BothInternational journal of molecular sciences · 2024Article
- Distribution rules of 8-mer spectra and characterization of evolution state in animal genome sequences.BMC genomics · 2024Article
- A chromosome-level genome assembly ofFrontiers in plant science · 2024Article
- The leaky gut and the gut microbiome in sepsis - targets in research and treatment.Clinical science (London, England : 1979) · 2023Article
- Draft Genome of Tanacetum Coccineum: Genomic Comparison of Closely Related Tanacetum-Family Plants.International journal of molecular sciences · 2022Article
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- Blood Bacteria-Free DNA in Septic Mice Enhances LPS-Induced Inflammation in Mice through Macrophage Response.International journal of molecular sciences · 2022Article
- A chromosome-anchored genome assembly for Lake Trout (Salvelinus namaycush).Molecular ecology resources · 2022Article
- Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT.PLoS computational biology · 2021Article
- Estimation of Genome Size in the Endemic SpeciesPlants (Basel, Switzerland) · 2021Article
- Measuring Genome Sizes Using Read-Depth, k-mers, and Flow Cytometry: Methodological Comparisons in Beetles (Coleoptera).G3 (Bethesda, Md.) · 2020Article
- Plasmid-mediated metronidazole resistance in Clostridioides difficile.Nature communications · 2020Article
- Assembly and Characterization of a Pathogen Strain Collection for Produce Safety Applications: Pre-growth Conditions Have a Larger Effect on Peroxyacetic Acid Tolerance Than Strain Diversity.Frontiers in microbiology · 2019Article
- Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.BMC genomics · 2018Article
- ATP hydrolysis provides functions that promote rejection of pairings between different copies of long repeated sequences.Nucleic acids research · 2017Article
- Draft Genome Sequence ofGenome announcements · 2017Article
- Genome analysis of Diploscapter coronatus: insights into molecular peculiarities of a nematode with parthenogenetic reproduction.BMC genomics · 2017Article
- Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement.Scientific reports · 2017Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe numerous classes of repeats often impede the assembly of genome sequences from the short reads provided by new sequencing technologies. We demonstrate a simple and rapid means to ascertain the repeat structure and total size of a bacterial or archaeal genome without the need for assembly by directly analyzing the abundances of distinct k-mers among reads.
resultsThe sensitivity of this procedure to resolve variation within a bacterial species is demonstrated: genome sizes and repeat structure of five environmental strains of E. coli from short Illumina reads were estimated by this method, and total genome sizes corresponded well with those obtained for the same strains by pulsed-field gel electrophoresis. In addition, this approach was applied to read-sets for completed genomes and shown to be accurate over a wide range of microbial genome sizes.
conclusionsApplication of these procedures, based solely on k-mer abundances in short read data sets, allows aspects of genome structure to be resolved that are not apparent from conventional short read assemblies. This knowledge of the repetitive content of genomes provides insights into genome evolution and diversity.
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