ArticleScientific reports2014
Alignment-free visualization of metagenomic data by nonlinear dimension reduction.
Article in Scientific reports, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Review
- KPop: accurate and scalable comparative analysis of microbial genomes by sequence embeddings.Genome biology · 2025Article
- Article
- Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing.Nature methods · 2021Article
- Ancient Metabolisms of a Thermophilic Subseafloor Bacterium.Frontiers in microbiology · 2021Article
- MetaBCC-LR: metagenomics binning by coverage and composition for long reads.Bioinformatics (Oxford, England) · 2020Article
- Autometa: automated extraction of microbial genomes from individual shotgun metagenomes.Nucleic acids research · 2019Article
- Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential.Nature communications · 2018Article
- Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.Nature biotechnology · 2018Article
- CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision.BMC bioinformatics · 2017Article
- Metagenome-Assembled Genome Sequences ofGenome announcements · 2017Article
- BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation.Nucleic acids research · 2017Article
- Interpreting Microbial Biosynthesis in the Genomic Age: Biological and Practical Considerations.Marine drugs · 2017Review
- Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics.Computational and structural biotechnology journal · 2017Review
- acdc - Automated Contamination Detection and Confidence estimation for single-cell genome data.BMC bioinformatics · 2016Article
- IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses.Genome biology · 2016Article
- Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome.Scientific reports · 2016Article
- Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes.Scientific reports · 2016Article
- Metagenomic Analysis Reveals Symbiotic Relationship among Bacteria in Microcystis-Dominated Community.Frontiers in microbiology · 2016Article
- Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract.Frontiers in microbiology · 2016Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The visualization of metagenomic data, especially without prior taxonomic identification of reconstructed genomic fragments, is a challenging problem in computational biology. An ideal visualization method should, among others, enable clear distinction of congruent groups of sequences of closely related taxa, be applicable to fragments of lengths typically achievable following assembly, and allow the efficient analysis of the growing amounts of community genomic sequence data. Here, we report a scalable approach for the visualization of metagenomic data that is based on nonlinear dimension reduction via Barnes-Hut Stochastic Neighbor Embedding of centered log-ratio transformed oligonucleotide signatures extracted from assembled genomic sequence fragments. The approach allows for alignment-free assessment of the data-inherent taxonomic structure, and it can potentially facilitate the downstream binning of genomic fragments into uniform clusters reflecting organismal origin. We demonstrate the performance of our approach by visualizing community genomic sequence data from simulated as well as groundwater, human-derived and marine microbial communities.
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