ArticleBMC genomics2017
Assembling metagenomes, one community at a time.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers, 1 of them a synthesis that pooled it.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
62 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Proposal of a health gut microbiome index based on a meta-analysis of Korean and global population datasets.Journal of microbiology (Seoul, Korea) · 2022Pooled it
- Multi-omics insights into bacterial and fungal bioremediation of Potentially Toxic Elements (PTEs): a critical overview of their applications.World journal of microbiology & biotechnology · 2026Review
- Efficient De Novo Assembly and Recovery of Microbial Genomes from Complex Metagenomes Using a Reduced Set of k-mers.Interdisciplinary sciences, computational life sciences · 2026Article
- Developing Effective Bioinoculant and Engineering Plant Microbiome for Climate Resilient Agriculture: Lessons Learned and Future Roadmap.Current microbiology · 2026Review
- HtPIP: High-throughput phage isolation platform increases diversity and reduces isolation time using multiple bacteria.Frontiers in microbiology · 2026Article
- Viral diversity in wild and urban rodents of Yunnan Province, China.Emerging microbes & infections · 2024Article
- Integrated large-scale metagenome assembly and multi-kingdom network analyses identify sex differences in the human nasal microbiome.Genome biology · 2024Article
- Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing.Nucleic acids research · 2024Article
- How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies.Microbial genomics · 2024Article
- Article
- Interpretation of vaginal metagenomic characteristics in different types of vaginitis.mSystems · 2024Article
- Unveiling the Microbial Realm with VEBA 2.0: A modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic, and viral multi-omics from either short- or long-read sequencing.bioRxiv : the preprint server for biology · 2024Article
- On the limits of 16S rRNA gene-based metagenome prediction and functional profiling.Microbial genomics · 2024Article
- Article
- Evaluation of multiple displacement amplification for metagenomic analysis of low biomass samples.ISME communications · 2024Article
- Comparative analysis of HiSeq3000 and BGISEQ-500 sequencing platform over whole genome sequencing metagenomics data.Genomics & informatics · 2023Article
- Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast.Scientific reports · 2023Article
- Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research.FEMS microbiology reviews · 2023Review
- Composition and function of the Galapagos penguin gut microbiome vary with age, location, and a putative bacterial pathogen.Scientific reports · 2023Article
- Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics.Computational and structural biotechnology journal · 2023Review
2 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
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMetagenomics allows unprecedented access to uncultured environmental microorganisms. The analysis of metagenomic sequences facilitates gene prediction and annotation, and enables the assembly of draft genomes, including uncultured members of a community. However, while several platforms have been developed for this critical step, there is currently no clear framework for the assembly of metagenomic sequence data.
resultsTo assist with selection of an appropriate metagenome assembler we evaluated the capabilities of nine prominent assembly tools on nine publicly-available environmental metagenomes, as well as three simulated datasets. Overall, we found that SPAdes provided the largest contigs and highest N50 values across 6 of the 9 environmental datasets, followed by MEGAHIT and metaSPAdes. MEGAHIT emerged as a computationally inexpensive alternative to SPAdes, assembling the most complex dataset using less than 500 GB of RAM and within 10 hours.
conclusionsWe found that assembler choice ultimately depends on the scientific question, the available resources and the bioinformatic competence of the researcher. We provide a concise workflow for the selection of the best assembly tool.
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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.