ArticlePloS one2014
IM-TORNADO: a tool for comparison of 16S reads from paired-end libraries.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers, 1 of them a synthesis that pooled it.
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Who cites it
65 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Multi-cohort ensemble learning framework for vaginal microbiome-based endometrial cancer detection.Frontiers in cellular and infection microbiology · 2025Pooled it
- Increasing Rumen Microbial Diversity in Goats Favours the Adaptation to High-Concentrate Diets With Minor Effects on Feed Utilization.Journal of animal physiology and animal nutrition · 2026Article
- Dynamic cholangiocyte responses in a murine model of reversible cholestasis: macrophage remodeling and NF-Y-mediated TGFβ1 expression.American journal of physiology. Gastrointestinal and liver physiology · 2025Article
- Enhancing rumen microbial diversity and its impact on energy and protein metabolism in forage-fed goats.Frontiers in veterinary science · 2023Article
- Potential Role of Inflammation-Promoting Biliary Microbiome in Primary Sclerosing Cholangitis and Cholangiocarcinoma.Cancers · 2022Article
- Administration of Human Derived Upper gut Commensal Prevotella histicola delays the onset of type 1 diabetes in NOD mice.BMC microbiology · 2022Article
- Concatenation of paired-end reads improves taxonomic classification of amplicons for profiling microbial communities.BMC bioinformatics · 2021Article
- Diverse and active archaea communities occur in non-disinfected drinking water systems-Less activity revealed in disinfected and hot water systems.Water research X · 2021Article
- Early life dietary intervention in dairy calves results in a long-term reduction in methane emissions.Scientific reports · 2021Article
- Inoculation with rumen fluid in early life accelerates the rumen microbial development and favours the weaning process in goats.Animal microbiome · 2021Article
- Transition of microbiota in chicken cecal droppings from commercial broiler farms.BMC veterinary research · 2021Article
- RFtest: A Robust and Flexible Community-Level Test for Microbiome Data Powerfully Detects Phylogenetically Clustered Signals.Frontiers in genetics · 2021Review
- Comparison of Periodontal Bacteria of Edo and Modern Periods Using Novel Diagnostic Approach for Periodontitis With Micro-CT.Frontiers in cellular and infection microbiology · 2021Article
- Characterization and Comparison of Intestinal Bacterial Microbiomes ofFrontiers in microbiology · 2021Article
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- Non-surgical treatment for periodontitis and peri-implantitis: longitudinal clinical and bacteriological findings-A case report with a 7-year follow-up evaluation.SAGE open medical case reports · 2021Article
- Age and environmental exposures influence the fecal bacteriome of young children with cystic fibrosis.Pediatric pulmonology · 2020Article
- 16S rRNA Gene Amplicon Sequence Data from Feces of Five Species of Wild Animals in Japan.Microbiology resource announcements · 2020Article
- 16S rRNA Gene Amplicon Sequence Data from Feces of Wild Deer (Cervus nippon) in Japan.Microbiology resource announcements · 2020Article
5 more citing papers are in PubMed but not listed here.
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PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
motivation16S rDNA hypervariable tag sequencing has become the de facto method for accessing microbial diversity. Illumina paired-end sequencing, which produces two separate reads for each DNA fragment, has become the platform of choice for this application. However, when the two reads do not overlap, existing computational pipelines analyze data from read separately and underutilize the information contained in the paired-end reads.
resultsWe created a workflow known as Illinois Mayo Taxon Organization from RNA Dataset Operations (IM-TORNADO) for processing non-overlapping reads while retaining maximal information content. Using synthetic mock datasets, we show that the use of both reads produced answers with greater correlation to those from full length 16S rDNA when looking at taxonomy, phylogeny, and beta-diversity. AVAILABILITY AND IMPLEMENTATION: IM-TORNADO is freely available at http://sourceforge.net/projects/imtornado and produces BIOM format output for cross compatibility with other pipelines such as QIIME, mothur, and phyloseq.
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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.