ArticleNucleic acids research2017
BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Effects of Resistant Starch on Symptoms, Fecal Markers, and Gut Microbiota in Parkinson's Disease - The RESISTA-PD Trial.Genomics, proteomics & bioinformatics · 2022Trial
- Advances in Shotgun Metagenomics for Cheese Microbiology: From Microbial Dynamics to Functional Insights.Foods (Basel, Switzerland) · 2026Review
- Review
- Profiling of Pharmaceutical Sludge Microbiome, Resistome and Secondary Metabolites Using Metagenomics.Indian journal of microbiology · 2025Article
- Solving genomic puzzles: computational methods for metagenomic binning.Briefings in bioinformatics · 2024Review
- AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides.BMC bioinformatics · 2024Article
- Investigation of the Microbiome of Industrial PDO Sfela Cheese and Its Artisanal Variants Using 16S rDNA Amplicon Sequencing and Shotgun Metagenomics.Foods (Basel, Switzerland) · 2024Article
- Microbiomes, diet flexibility, and the spread of a beetle parasite of honey bees.Frontiers in microbiology · 2024Article
- BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes.Microbiome · 2023Article
- Cuticle supplementation and nitrogen recycling by a dual bacterial symbiosis in a family of xylophagous beetles.The ISME journal · 2023Article
- Genomic Assessment of the Contribution of theInternational journal of molecular sciences · 2023Article
- Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses.Viruses · 2023Review
- The toxins of vertically transmittedFrontiers in microbiology · 2023Article
- Recovery and Analysis of Long-Read Metagenome-Assembled Genomes.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Contamination detection and microbiome exploration with GRIMER.GigaScience · 2022Article
- Non-random genetic alterations in the cyanobacterium Nostoc sp. exposed to space conditions.Scientific reports · 2022Article
- Binning long reads in metagenomics datasets using composition and coverage information.Algorithms for molecular biology : AMB · 2022Article
- Comparison of the Microbiome of Artisanal Homemade and Industrial Feta Cheese through Amplicon Sequencing and Shotgun Metagenomics.Microorganisms · 2022Article
- Whole genome sequencing of cyanobacteriumiScience · 2022Article
- Highly transmissible cytoplasmic incompatibility by the extracellular insect symbiontiScience · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metagenomics-based studies of mixed microbial communities are impacting biotechnology, life sciences and medicine. Computational binning of metagenomic data is a powerful approach for the culture-independent recovery of population-resolved genomic sequences, i.e. from individual or closely related, constituent microorganisms. Existing binning solutions often require a priori characterized reference genomes and/or dedicated compute resources. Extending currently available reference-independent binning tools, we developed the BusyBee Web server for the automated deconvolution of metagenomic data into population-level genomic bins using assembled contigs (Illumina) or long reads (Pacific Biosciences, Oxford Nanopore Technologies). A reversible compression step as well as bootstrapped supervised binning enable quick turnaround times. The binning results are represented in interactive 2D scatterplots. Moreover, bin quality estimates, taxonomic annotations and annotations of antibiotic resistance genes are computed and visualized. Ground truth-based benchmarks of BusyBee Web demonstrate comparably high performance to state-of-the-art binning solutions for assembled contigs and markedly improved performance for long reads (median F1 scores: 70.02-95.21%). Furthermore, the applicability to real-world metagenomic datasets is shown. In conclusion, our reference-independent approach automatically bins assembled contigs or long reads, exhibits high sensitivity and precision, enables intuitive inspection of the results, and only requires FASTA-formatted input. The web-based application is freely accessible at: https://ccb-microbe.cs.uni-saarland.de/busybee.
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