ArticlePloS one2012
Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 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.
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Who cites it
34 citing papers in PubMed, 51 citations in OpenAlex.
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- Early antibiotic exposure and vaccine immune responses in preterm infants: potential sex-specific differences.Gut microbes · 2026Observational
- SigAlign: an alignment algorithm guided by explicit similarity criteria.Nucleic acids research · 2024Article
- Evaluation of the lignocellulose degradation potential of Mediterranean forests soil microbial communities through diversity and targeted functional metagenomics.Frontiers in microbiology · 2023Article
- An Introduction to Whole-Metagenome Shotgun Sequencing Studies.Methods in molecular biology (Clifton, N.J.) · 2021Review
- A Targeted Metagenomics Approach to Study the Diversity of Norovirus GII in Shellfish Implicated in Outbreaks.Viruses · 2020Article
- IgA regulates the composition and metabolic function of gut microbiota by promoting symbiosis between bacteria.The Journal of experimental medicine · 2018Article
- Towards predicting the environmental metabolome from metagenomics with a mechanistic model.Nature microbiology · 2018Article
- Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics.PloS one · 2017Article
- Large-scale machine learning for metagenomics sequence classification.Bioinformatics (Oxford, England) · 2016Article
- The role of the intestinal microbiota in type 1 diabetes mellitus.Nature reviews. Endocrinology · 2016Review
- Metagenomic Approach for Identification of the Pathogens Associated with Diarrhea in Stool Specimens.Journal of clinical microbiology · 2016Article
- Using populations of human and microbial genomes for organism detection in metagenomes.Genome research · 2015Article
- Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment.Nature communications · 2015Article
- Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling.Applied and environmental microbiology · 2014Article
- The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease.Cell host & microbe · 2014Article
- Exploration of bacterial community classes in major human habitats.Genome biology · 2014Article
- Live genomics for pathogen monitoring in public health.Pathogens (Basel, Switzerland) · 2014Article
Corrections and comments
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Authors and funding
11 authors at 5 institutions in 1 country.
Funding
Abstract
The Human Microbiome Project (HMP) aims to characterize the microbial communities of 18 body sites from healthy individuals. To accomplish this, the HMP generated two types of shotgun data: reference shotgun sequences isolated from different anatomical sites on the human body and shotgun metagenomic sequences from the microbial communities of each site. The alignment strategy for characterizing these metagenomic communities using available reference sequence is important to the success of HMP data analysis. Six next-generation aligners were used to align a community of known composition against a database comprising reference organisms known to be present in that community. All aligners report nearly complete genome coverage (>97%) for strains with over 6X depth of coverage, however they differ in speed, memory requirement and ease of use issues such as database size limitations and supported mapping strategies. The selected aligner was tested across a range of parameters to maximize sensitivity while maintaining a low false positive rate. We found that constraining alignment length had more impact on sensitivity than does constraining similarity in all cases tested. However, when reference species were replaced with phylogenetic neighbors, similarity begins to play a larger role in detection. We also show that choosing the top hit randomly when multiple, equally strong mappings are available increases overall sensitivity at the expense of taxonomic resolution. The results of this study identified a strategy that was used to map over 3 tera-bases of microbial sequence against a database of more than 5,000 reference genomes in just over a month.
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What OpenQuestion holds
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.