ArticleBriefings in bioinformatics2019
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes.
Article in Briefings in bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
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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.
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Who cites it
78 citing papers in PubMed.
- META-DIFF: a k-mer-based pipeline that detects differentially abundant sequences in metagenomics whole genome sequencing.Scientific reports · 2026Article
- Article
- Troubleshooting common errors in assemblies of long-read metagenomes.Nature biotechnology · 2026Article
- Reference-guided assembly of metagenomes with MetaCompass.Cell reports methods · 2025Article
- Metagenomic Applications to Herbivore Gut Microbiomes: A Comprehensive Review of Microbial Diversity and Host Interactions.Animals : an open access journal from MDPI · 2025Review
- Variation of and associations with the depth and evenness of sequencing coverage in archived plastid genomes.Scientific reports · 2025Article
- Variation of and associations with the depth and evenness of sequencing coverage in archived plastid genomes.Research square · 2025Article
- Genomic characterization of antimicrobial resistance and mobile genetic elements in swine gut bacteria isolated from a Canadian research farm.Animal microbiome · 2025Article
- Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data.mBio · 2025Article
- Current Approaches and Implications in Discovery of Novel Bioactive Products from Microbial Sources.Current microbiology · 2025Review
- Analysis of metagenomic data.Nature reviews. Methods primers · 2025Article
- Unlocking the Potential of Metagenomics with the PacBio High-Fidelity Sequencing Technology.Microorganisms · 2024Review
- Article
- Insights into mycobacteriome composition in Mycobacterium bovis-infected African buffalo (Syncerus caffer) tissue samples.Scientific reports · 2024Article
- Unveiling microbial diversity: harnessing long-read sequencing technology.Nature methods · 2024Review
- Nanopore and Illumina sequencing reveal different viral populations from human gut samples.Microbial genomics · 2024Article
- - Invited Review - Understanding the functionality of the rumen microbiota: searching for better opportunities for rumen microbial manipulation.Animal bioscience · 2024Article
- Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads.Microbial genomics · 2024Article
- KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2024Article
- Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements.PeerJ · 2024Article
18 more citing papers are in PubMed but not listed here.
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7 authors.
Funding
Abstract
Metagenomic samples are snapshots of complex ecosystems at work. They comprise hundreds of known and unknown species, contain multiple strain variants and vary greatly within and across environments. Many microbes found in microbial communities are not easily grown in culture making their DNA sequence our only clue into their evolutionary history and biological function. Metagenomic assembly is a computational process aimed at reconstructing genes and genomes from metagenomic mixtures. Current methods have made significant strides in reconstructing DNA segments comprising operons, tandem gene arrays and syntenic blocks. Shorter, higher-throughput sequencing technologies have become the de facto standard in the field. Sequencers are now able to generate billions of short reads in only a few days. Multiple metagenomic assembly strategies, pipelines and assemblers have appeared in recent years. Owing to the inherent complexity of metagenome assembly, regardless of the assembly algorithm and sequencing method, metagenome assemblies contain errors. Recent developments in assembly validation tools have played a pivotal role in improving metagenomics assemblers. Here, we survey recent progress in the field of metagenomic assembly, provide an overview of key approaches for genomic and metagenomic assembly validation and demonstrate the insights that can be derived from assemblies through the use of assembly validation strategies. We also discuss the potential for impact of long-read technologies in metagenomics. We conclude with a discussion of future challenges and opportunities in the field of metagenomic assembly and validation.
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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.