ArticleBMC genomics2019
MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Environmental context reveals distinct regulatory patterns in field-grown versus in vitro symbiotic protocorms of Dactylorhiza majalis (Orchidaceae).BMC plant biology · 2026Article
- Gut Hi-C metagenomes of severe COVID-19 patients: bacteria and yeast involved in gut-lung axis.mSphere · 2026Article
- Report of the fourth conference on next-generation sequencing (NGS) for adventitious virus detection in biologics for humans and animals: Validation and implementation of NGS.Biologicals : journal of the International Association of Biological Standardization · 2025Article
- Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases.Microbiome · 2025Article
- Ecological divergence of sibling allopolyploid marsh orchids is associated with species specific plasticity and distinct fungal communities.The Plant journal : for cell and molecular biology · 2025Article
- Article
- RUBICON: a framework for designing efficient deep learning-based genomic basecallers.Genome biology · 2024Article
- Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem.Microbiology spectrum · 2023Article
- The International Virus Bioinformatics Meeting 2023.Viruses · 2023Article
- Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash.Genome research · 2023Article
- The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice.Nature microbiology · 2023Article
- The gut microbiota in multiple sclerosis varies with disease activity.Genome medicine · 2023Article
- Multi-kingdom gut microbiota analyses define COVID-19 severity and post-acute COVID-19 syndrome.Nature communications · 2022Article
- Development and Validation of a Bioinformatic Workflow for the Rapid Detection of Viruses in Biosecurity.Viruses · 2022Article
- An overview of gastrointestinal diseases in patients with COVID-19: A narrative review.Medicine · 2022Review
- GenBank as a source to monitor and analyze Host-Microbiome data.Bioinformatics (Oxford, England) · 2022Article
- Exposure to Trypanosoma parasites induces changes in the microbiome of the Chagas disease vector Rhodnius prolixus.Microbiome · 2022Article
- From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures.Computational and structural biotechnology journal · 2022Review
- Article
- Hi-C Metagenomics in the ICU: Exploring Clinically Relevant Features of Gut Microbiome in Chronically Critically Ill Patients.Frontiers in microbiology · 2021Article
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Authors and funding
7 authors.
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Abstract
backgroundHigh throughput sequencing has spurred the development of metagenomics, which involves the direct analysis of microbial communities in various environments such as soil, ocean water, and the human body. Many existing methods based on marker genes or k-mers have limited sensitivity or are too computationally demanding for many users. Additionally, most work in metagenomics has focused on bacteria and archaea, neglecting to study other key microbes such as viruses and eukaryotes.
resultsHere we present a method, MiCoP (Microbiome Community Profiling), that uses fast-mapping of reads to build a comprehensive reference database of full genomes from viruses and eukaryotes to achieve maximum read usage and enable the analysis of the virome and eukaryome in each sample. We demonstrate that mapping of metagenomic reads is feasible for the smaller viral and eukaryotic reference databases. We show that our method is accurate on simulated and mock community data and identifies many more viral and fungal species than previously-reported results on real data from the Human Microbiome Project.
conclusionsMiCoP is a mapping-based method that proves more effective than existing methods at abundance profiling of viruses and eukaryotes in metagenomic samples. MiCoP can be used to detect the full diversity of these communities. The code, data, and documentation are publicly available on GitHub at: https://github.com/smangul1/MiCoP .
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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.