ArticlePloS one2012
Assessment of metagenomic assembly using simulated next generation sequencing data.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 154 papers.
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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.
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Who cites it
154 citing papers in PubMed.
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- Comprehensive in silico analysis of eggNOG-annotated orthologous genes infers functional dynamics and energy metabolism in the microbiome of Abutilon fruticosum.BMC plant biology · 2026Article
- Rhizospheric glycosyltransferase repertoires as a resource for enabling sustainable bioprocessing and green biocatalyst discovery.Scientific reports · 2026Article
- Shotgun Metagenomics Reveals Microbial Diversity, Resistome, and Plasmidome in Dairy Cattle Feces.Veterinary sciences · 2026Article
- Functional potential of archaeal KEGG enzymes in the Moringa oleifera rhizosphere revealed by metagenomic analysis.BMC genomics · 2026Article
- Effects of legume-based rotation on subsequent sorghum rhizosphere microbial communities and their drought tolerance-related genes.Environmental microbiome · 2026Article
- Microbial community characterization in semi-hydroponic systems of Starbor kale (Current research in microbial sciences · 2026Article
- Organic amendments boost maize yield (Frontiers in plant science · 2026Article
- Metagenomic analysis of the community structure and functional potential ofFrontiers in microbiology · 2026Article
- Metagenomic and metabolomic profiling in primary aldosteronism with coexisting obstructive sleep apnea.Frontiers in endocrinology · 2026Observational
- Gut microbiota and metabolic status during pregnancy in captive Asian elephants.Frontiers in veterinary science · 2026Article
- Gut microbiome is associated with stereotypic behavior of the giant panda (Ailuropoda melanoleuca).PloS one · 2026Article
- Differences in ginseng quality and soil characteristics in different growth modes ofFrontiers in plant science · 2026Article
- Effects of different additives and chopping lengths on the biosafety of Sophora Davidii silage.BMC microbiology · 2025Article
- Dynamics of the gut microbiome and resistome in response to prophylactic antibiotic treatment in post-surgical giant pandas.Scientific reports · 2025Article
- ganon2: up-to-date and scalable metagenomics analysis.NAR genomics and bioinformatics · 2025Article
- Multi-Metagenome Analysis Unravels Community Collapse After Sampling and Hints the Cultivation Strategy of CPR Bacteria in Groundwater.Microorganisms · 2025Article
- Comprehensive analysis of orthologous genes reveals functional dynamics and energy metabolism in the rhizospheric microbiome of Moringa oleifera.Functional & integrative genomics · 2025Article
- Differences in Microbial Community Structure Determine the Functional Specialization of Gut Segments ofMicroorganisms · 2025Article
94 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Due to the complexity of the protocols and a limited knowledge of the nature of microbial communities, simulating metagenomic sequences plays an important role in testing the performance of existing tools and data analysis methods with metagenomic data. We developed metagenomic read simulators with platform-specific (Sanger, pyrosequencing, Illumina) base-error models, and simulated metagenomes of differing community complexities. We first evaluated the effect of rigorous quality control on Illumina data. Although quality filtering removed a large proportion of the data, it greatly improved the accuracy and contig lengths of resulting assemblies. We then compared the quality-trimmed Illumina assemblies to those from Sanger and pyrosequencing. For the simple community (10 genomes) all sequencing technologies assembled a similar amount and accurately represented the expected functional composition. For the more complex community (100 genomes) Illumina produced the best assemblies and more correctly resembled the expected functional composition. For the most complex community (400 genomes) there was very little assembly of reads from any sequencing technology. However, due to the longer read length the Sanger reads still represented the overall functional composition reasonably well. We further examined the effect of scaffolding of contigs using paired-end Illumina reads. It dramatically increased contig lengths of the simple community and yielded minor improvements to the more complex communities. Although the increase in contig length was accompanied by increased chimericity, it resulted in more complete genes and a better characterization of the functional repertoire. The metagenomic simulators developed for this research are freely available.
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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.