ReviewGenome research2020
Accurate and complete genomes from metagenomes.
Review in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 234 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
234 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A gut microbial signature for combination immune checkpoint blockade across cancer types.Nature medicine · 2024Pooled it
- Integrating multi-omics technologies to decipher microbiome functions.Nature communications · 2026Review
- Widespread genomic islands are hotspots of genome variations and mosaicism in giant viruses.Nature communications · 2026Article
- Fast-nnt: fast, reproducible, and scalable neighbour network analysis in R, Python, and CLI.Bioinformatics (Oxford, England) · 2026Article
- Proteobacteria with chemosynthetic potential are highly prevalent in the gills of Hypoplectrus reef fishes.PLoS genetics · 2026Article
- Bioactive molecules unearthed by terabase-scale long-read sequencing of a soil metagenome.Nature biotechnology · 2026Article
- Phylogenize2: robust phylogenetic methods link genes to phenotypes across host-associated and environmental microbiomes.bioRxiv : the preprint server for biology · 2026Article
- Jumbo circular extrachromosomal elements of methane-oxidizing archaea with variably extensive metabolic and defense gene repertoires.Nature communications · 2026Article
- Draft genome sequence CR-NGP1 strain of 'Candidatus Liberibacter asiaticus' (CLas) from the host Citrus reticulata (Nagpur mandarin) from Central India.World journal of microbiology & biotechnology · 2026Article
- Unbinned contigs expand known diversity in the global microbiome.Nature microbiology · 2026Article
- Integrated metagenomic analysis of bacteriomes associated with beach-cast seaweeds reveals metabolic potential for biotechnological and environmental applications.Scientific reports · 2026Article
- Effects of heat-assisted sample desiccation on microbiome surveys.Environmental microbiome · 2026Article
- Genome-resolved metagenomic survey of 500 samples from 56 hot springs across the Western US.Scientific data · 2026Article
- The genomic history of Streptococcus mutans from the Mesolithic until modern times.Genome biology · 2026Article
- High-quality metagenome assembly from nanopore reads with nanoMDBG.Nature communications · 2026Article
- CAMP: a modular metagenomics analysis system for integrated multistep data exploration.NAR genomics and bioinformatics · 2026Article
- A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination.bioRxiv : the preprint server for biology · 2026Article
- Animal-associated jumbo phages as widespread and active modulators of gut microbiome ecology and metabolism.Science advances · 2026Article
- Troubleshooting common errors in assemblies of long-read metagenomes.Nature biotechnology · 2026Article
- Metagenomic Assembly and Gene Prediction.Methods in molecular biology (Clifton, N.J.) · 2026Article
174 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Genomes are an integral component of the biological information about an organism; thus, the more complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures, and the first reported sequences were manually curated to completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation by obtaining metagenome-assembled genomes (MAGs); but gaps, local assembly errors, chimeras, and contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome curation to improve and, in some cases, achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably some are from very complex systems such as soil and sediment. Through analysis of about 7000 published complete bacterial isolate genomes, we verify the value of cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. The analysis of cumulative GC skew identified potential misassemblies in some reference genomes of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary analyses can be based on very high-quality genomes.
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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.