ArticleBMC genomics2010
Finishing genomes with limited resources: lessons from an ensemble of microbial genomes.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed.
- Manual Annotation Studio (MAS): a collaborative platform for manual functional annotation of viral and microbial genomes.BMC genomics · 2021Article
- Multiplexed Non-barcoded Long-Read Sequencing and Assembling Genomes of Bacillus Strains in Error-Free Simulations.Current microbiology · 2020Article
- riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions.Nucleic acids research · 2018Article
- Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.BMC genomics · 2018Article
- ImproveAssembly - Tool for identifying new gene products and improving genome assembly.PloS one · 2018Article
- Benefits of Genomic Insights and CRISPR-Cas Signatures to Monitor Potential Pathogens across Drinking Water Production and Distribution Systems.Frontiers in microbiology · 2017Article
- Multi-CAR: a tool of contig scaffolding using multiple references.BMC bioinformatics · 2016Article
- On the study of microbial transcriptomes using second- and third-generation sequencing technologies.Journal of microbiology (Seoul, Korea) · 2016Review
- WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data.BMC bioinformatics · 2015Article
- Recovering full-length viral genomes from metagenomes.Frontiers in microbiology · 2015Review
- Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences.Bioinformatics (Oxford, England) · 2014Article
- Comparative analysis of Klebsiella pneumoniae genomes identifies a phospholipase D family protein as a novel virulence factor.BMC biology · 2014Article
- Article
- Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing.Frontiers in microbiology · 2014Article
- Cytoplasmic male sterility-associated chimeric open reading frames identified by mitochondrial genome sequencing of four Cajanus genotypes.DNA research : an international journal for rapid publication of reports on genes and genomes · 2013Article
- De novo likelihood-based measures for comparing genome assemblies.BMC research notes · 2013Article
- Genome Sequencing of Four Strains of Rickettsia prowazekii, the Causative Agent of Epidemic Typhus, Including One Flying Squirrel Isolate.Genome announcements · 2013Article
- Beginner's guide to comparative bacterial genome analysis using next-generation sequence data.Microbial informatics and experimentation · 2013Article
- Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.BMC genomics · 2013Article
- BAIT: Organizing genomes and mapping rearrangements in single cells.Genome medicine · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
While new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has still remained elusive. Due to shorter read lengths and limitations in library construction protocols, shotgun sequencing and assembly based on these technologies often results in fragmented assemblies. Correspondingly, while draft assemblies can be obtained in days, finishing can take many months and hence the time and effort can only be justified for high-priority genomes and in large sequencing centers. In this work, we revisit this issue in light of our own experience in producing finished and nearly-finished genomes for a range of microbial species in a small-lab setting. These genomes were finished with surprisingly little investments in terms of time, computational effort and lab work, suggesting that the increased access to sequencing might also eventually lead to a greater proportion of finished genomes from small labs and genomics cores.
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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.