ArticleGenome biology2013
Reducing assembly complexity of microbial genomes with single-molecule sequencing.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 226 papers.
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Who cites it
226 citing papers in PubMed.
- Quantitative comparison of fungal genome assembly strategies using short and long reads from simulated and empirical sequencing data.Microbial genomics · 2026Article
- LORA: a polymorphic multi-sample long read assembly pipeline.NAR genomics and bioinformatics · 2026Article
- From contiguity to accuracy: Validation-centered perspectives on bacterial genome assembly.Journal of microbiology (Seoul, Korea) · 2026Review
- De-novo assembly of 82 bacterial genomes using Nanopore sequencing and prediction of biosynthetic capacity.Scientific data · 2026Article
- Review
- Troubleshooting common errors in assemblies of long-read metagenomes.Nature biotechnology · 2026Article
- Probiogenomics as a Computational Biotechnology Framework: Safety-Gated Genome Analytics for Candidate Probiotic Prioritization and Validation.Computational and structural biotechnology journal · 2026Review
- Analysis of the complete genome sequence ofMicrobiology resource announcements · 2025Article
- Reference-guided assembly of metagenomes with MetaCompass.Cell reports methods · 2025Article
- Autocycler: long-read consensus assembly for bacterial genomes.Bioinformatics (Oxford, England) · 2025Article
- Article
- Whole genome sequencing, characterization and analysis of coronene degrading bacterial strain Halomonas elongata.PloS one · 2025Article
- Rational construction of genome-minimizedSynthetic and systems biotechnology · 2024Article
- Genome assembly in the telomere-to-telomere era.Nature reviews. Genetics · 2024Review
- A practical guide and Galaxy workflow to avoid inter-plasmidic repeat collapse and false gene loss in Unicycler's hybrid assemblies.Microbial genomics · 2024Article
- Next generation plant biostimulants & genome sequencing strategies for sustainable agriculture development.Frontiers in microbiology · 2024Review
- Trio-binning of a hinny refines the comparative organization of the horse and donkey X chromosomes and reveals novel species-specific features.Scientific reports · 2023Article
- Development of a novel streamlined workflow (AACRE) and database (inCREDBle) for genomic analysis of carbapenem-resistant Enterobacterales.Microbial genomics · 2023Article
- Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi.Communications biology · 2023Article
- A high fidelity approach to assembling the complex Borrelia genome.BMC genomics · 2023Article
166 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem.
resultsTo measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads.
conclusionsAutomated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization.
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