ArticleScientific reports2016
Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 132 papers, 1 of them a synthesis that pooled it.
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Who cites it
132 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Systematic Review: Long-Read Sequencing in Algal Studies.International journal of molecular sciences · 2026Pooled it
- Improving metagenome binning by integrating intrinsic features and taxonomy.Nature biotechnology · 2026Article
- Exploring sagebrush leaf microbial metagenomes from deep, host-derived sequencing.Microbiology spectrum · 2026Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Evolutionary assembly of a unique purple-green photosymbiosis revealed by expanded ciliate diversity.The ISME journal · 2026Article
- Microbial Omics.Progress in molecular and subcellular biology · 2026Review
- Nuclear genome assembly and annotation for the phagotrophic green alga Nephroselmis pyriformis.Journal of phycology · 2025Article
- Metabolic Potential of Candidatus Saccharimonadia Including Rare Lineages in Activated Sludge.Environmental microbiology reports · 2025Article
- Putative promiscuous symbionts in deep-sea corals and crinoids may contribute to nitrogen cycling.Microbiome · 2025Article
- Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies.Molecular ecology resources · 2025Article
- Highly-accurate prediction of colorectal cancer through low abundance uncultivated genomes recovered using metagenomic co-assembly and binning approach.BMC cancer · 2025Article
- De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution.Environmental microbiome · 2025Article
- Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data.mBio · 2025Article
- Functional division of labor in motility, lignocellulose digestion, and nitrogen metabolism revealed for the Mixotricha paradoxa holobiont.The ISME journal · 2025Article
- Metagenomic Insights into Candidatus Scalindua in a Long-term Cultivated Marine Anammox Consortium: The Important Role of Tetrahydrofolate-mediated Carbon Fixation.Microbes and environments · 2025Article
- Visualizing metagenomic and metatranscriptomic data: A comprehensive review.Computational and structural biotechnology journal · 2024Review
- Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut.Cell systems · 2024Article
- Molecular diversity of green-colored microbial mats from hot springs of northern Japan.Extremophiles : life under extreme conditions · 2024Article
- Metagenome-assembled microbial genomes from Parkinson's disease fecal samples.Scientific reports · 2024Article
- Solving genomic puzzles: computational methods for metagenomic binning.Briefings in bioinformatics · 2024Review
72 more citing papers are in PubMed but not listed here.
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Metagenomics, the application of shotgun sequencing, facilitates the reconstruction of the genomes of individual species from natural environments. A major challenge in the genome recovery domain is to agglomerate or 'bin' sequences assembled from metagenomic reads into individual groups. Metagenomic binning without consideration of reference sequences enables the comprehensive discovery of new microbial organisms and aids in the microbial genome reconstruction process. Here we present MyCC, an automated binning tool that combines genomic signatures, marker genes and optional contig coverages within one or multiple samples, in order to visualize the metagenomes and to identify the reconstructed genomic fragments. We demonstrate the superior performance of MyCC compared to other binning tools including CONCOCT, GroopM, MaxBin and MetaBAT on both synthetic and real human gut communities with a small sample size (one to 11 samples), as well as on a large metagenome dataset (over 250 samples). Moreover, we demonstrate the visualization of metagenomes in MyCC to aid in the reconstruction of genomes from distinct bins. MyCC is freely available at http://sourceforge.net/projects/sb2nhri/files/MyCC/.
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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.