ArticleFrontiers in genetics2019
An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs.
Article in Frontiers in genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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75 citing papers in PubMed.
- Physiology, functional genomics, and proteomics ofApplied and environmental microbiology · 2026Article
- A cooperative cobalamide biosynthesis guild in the endosphere of the edible aquatic plant Wolffia globosa Mankai.Environmental microbiome · 2026Article
- In Vitro Degradation of Chlorpyrifos by the Ruminal Microbes: Insights from the Rumen Metagenome.Microorganisms · 2026Article
- GenomeDepot: data management system for microbial comparative genomics.Bioinformatics advances · 2026Article
- Acetate to caproate: metagenomic insights into functional shifts in a methane-arrested anaerobic bioreactor.FEMS microbes · 2026Article
- Microbial community structure, functional potential, probiotic signatures, and MAG reconstruction of fermented bamboo shoots from Northeast India.FEMS microbes · 2026Article
- annoreport: an interactive tool for metagenome annotation.Bioinformatics advances · 2026Article
- Deep-sea viral diversity and their role in host metabolism of complex organic matter.Nature communications · 2025Article
- Metagenomic report of element-microbe synergy and xenobiotic detoxification in the sacred waters of Khecheopalri lake, Eastern Himalaya.BMC microbiology · 2025Article
- Modeling reveals a metabolic basis of competition amongmSystems · 2025Article
- Transcriptomic Analyses Unveil Hydrocarbon Degradation Mechanisms in a Novel Polar Rhodococcus sp. Strain R1B_2T From a High Arctic Intertidal Zone Exposed to Ultra-Low Sulphur Fuel Oil.Environmental microbiology reports · 2025Article
- Vibrio pectenicida strain FHCF-3 is a causative agent of sea star wasting disease.Nature ecology & evolution · 2025Article
- Proteomic evidence for aerobic methane production in groundwater by methylotrophic Methylotenera.The ISME journal · 2025Article
- Influences of fluctuating nutrient loadings on nitrate-reducing microorganisms in rivers.ISME communications · 2025Article
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- Analysis of metagenomic data.Nature reviews. Methods primers · 2025Article
- Selective enrichment of high-affinity clade II NISME communications · 2025Article
- Visualizing metagenomic and metatranscriptomic data: A comprehensive review.Computational and structural biotechnology journal · 2024Review
- Ecology and biogeochemistry of the microbial underworld in two sister soda lakes.Environmental microbiome · 2024Article
15 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Here, we describe MetaErg, a standalone and fully automated metagenome and metaproteome annotation pipeline. Annotation of metagenomes is challenging. First, metagenomes contain sequence data of many organisms from all domains of life. Second, many of these are from understudied lineages, encoding genes with low similarity to experimentally validated reference genes. Third, assembly and binning are not perfect, sometimes resulting in artifactual hybrid contigs or genomes. To address these challenges, MetaErg provides graphical summaries of annotation outcomes, both for the complete metagenome and for individual metagenome-assembled genomes (MAGs). It performs a comprehensive annotation of each gene, including taxonomic classification, enabling functional inferences despite low similarity to reference genes, as well as detection of potential assembly or binning artifacts. When provided with metaproteome information, it visualizes gene and pathway activity using sequencing coverage and proteomic spectral counts, respectively. For visualization, MetaErg provides an HTML interface, bringing all annotation results together, and producing sortable and searchable tables, collapsible trees, and other graphic representations enabling intuitive navigation of complex data. MetaErg, implemented in Perl, HTML, and JavaScript, is a fully open source application, distributed under Academic Free License at https://github.com/xiaoli-dong/metaerg. MetaErg is also available as a docker image at https://hub.docker.com/r/xiaolidong/docker-metaerg.
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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.