ArticleBioinformatics (Oxford, England)2014
Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
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- Phylogenomics and genetic analysis of solvent-producing Clostridium species.Scientific data · 2024Article
- De novo genome assembly and comparative genomics for the colonial ascidian Botrylloides violaceus.G3 (Bethesda, Md.) · 2023Article
- Proposal to classifyFrontiers in microbiology · 2023Article
- Mining of key genes for cold adaptation fromFrontiers in microbiology · 2023Article
- Hybrid Genomic Analysis ofMicroorganisms · 2022Article
- Reference Genome Assembly of the Big Berry Manzanita (Arctostaphylos glauca).The Journal of heredity · 2022Article
- Identification of the Biosynthetic Gene Cluster for the Organoarsenical Antibiotic Arsinothricin.Microbiology spectrum · 2021Article
- Cultivating the Bacterial Microbiota ofmSystems · 2021Article
- Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria.Cellular and molecular life sciences : CMLS · 2021Review
- Rapid, robust plasmid verification by de novo assembly of short sequencing reads.Nucleic acids research · 2020Article
- Toward a more holistic method of genome assembly assessment.BMC bioinformatics · 2020Review
- Challenges and opportunities for strain verification by whole-genome sequencing.Scientific reports · 2020Article
- Ultraplexing: increasing the efficiency of long-read sequencing for hybrid assembly with k-mer-based multiplexing.Genome biology · 2020Article
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- Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology.Scientific reports · 2019Article
2 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
motivationTo assess the potential of different types of sequence data combined with de novo and hybrid assembly approaches to improve existing draft genome sequences.
resultsIllumina, 454 and PacBio sequencing technologies were used to generate de novo and hybrid genome assemblies for four different bacteria, which were assessed for quality using summary statistics (e.g. number of contigs, N50) and in silico evaluation tools. Differences in predictions of multiple copies of rDNA operons for each respective bacterium were evaluated by PCR and Sanger sequencing, and then the validated results were applied as an additional criterion to rank assemblies. In general, assemblies using longer PacBio reads were better able to resolve repetitive regions. In this study, the combination of Illumina and PacBio sequence data assembled through the ALLPATHS-LG algorithm gave the best summary statistics and most accurate rDNA operon number predictions. This study will aid others looking to improve existing draft genome assemblies. AVAILABILITY AND IMPLEMENTATION: All assembly tools except CLC Genomics Workbench are freely available under GNU General Public License. CONTACT: brownsd@ornl.gov SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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