ArticleMicrobiome2019
CAMISIM: simulating metagenomes and microbial communities.
Article in Microbiome, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 128 papers, 2 of them syntheses that pooled it.
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Who cites it
128 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models.Nature microbiology · 2026Pooled it
- Effect of Operational Parameters on the Cultivation of the Gut Microbiome in Continuous Bioreactors Inoculated with Feces: A Systematic Review.Journal of agricultural and food chemistry · 2023Pooled it
- Temporal dynamics of gut biosynthetic gene clusters link persistent colonization and engraftment in fecal microbiota transplantation.Gut microbes · 2026Article
- Human gut flagellome profiling using FlaPro reveals TLR5-related phenotype-specific alterations in IBD.Gut microbes · 2026Article
- metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.Gut microbes · 2026Article
- META-DIFF: a k-mer-based pipeline that detects differentially abundant sequences in metagenomics whole genome sequencing.Scientific reports · 2026Article
- MetaStrainer: accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples.Bioinformatics (Oxford, England) · 2026Article
- Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis.Nature microbiology · 2026Article
- Flush With Data (or) Optimizing and Validating the Efficacy of Free and Computationally Simple 16S Metabarcoding Approaches for Use in Wastewater Surveillance.Environmental microbiology · 2026Article
- Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery.Nature communications · 2026Article
- End-to-end evaluation of pipelines for metagenome-assembled genomes reveals hidden performance gaps.bioRxiv : the preprint server for biology · 2026Article
- ChloroScan: Recovering Plastid Genome Bins From Metagenomic Data.Molecular ecology resources · 2026Article
- Article
- Accurate plasmid reconstruction from metagenomics data using assembly-alignment graphs and contrastive learning.Nature biotechnology · 2026Article
- Strain-level metagenomic profiling using pangenome graphs with PanTax.Genome research · 2026Article
- MHASS: Microbiome HiFi Amplicon Sequencing Simulator.Bioinformatics (Oxford, England) · 2026Article
- Metagenomic next-generation sequencing: new horizons in microbiology.Frontiers in cellular and infection microbiology · 2026Review
- Article
- Comparative metagenomics using pan-metagenomic graphs.bioRxiv : the preprint server for biology · 2025Article
- Evaluation of metagenome binning: advances and challenges.Briefings in bioinformatics · 2025Article
68 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
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundShotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, to effectively assess the performance of metagenomic analysis software, a wide range of benchmark data sets are required.
resultsWe describe the CAMISIM microbial community and metagenome simulator. The software can model different microbial abundance profiles, multi-sample time series, and differential abundance studies, includes real and simulated strain-level diversity, and generates second- and third-generation sequencing data from taxonomic profiles or de novo. Gold standards are created for sequence assembly, genome binning, taxonomic binning, and taxonomic profiling. CAMSIM generated the benchmark data sets of the first CAMI challenge. For two simulated multi-sample data sets of the human and mouse gut microbiomes, we observed high functional congruence to the real data. As further applications, we investigated the effect of varying evolutionary genome divergence, sequencing depth, and read error profiles on two popular metagenome assemblers, MEGAHIT, and metaSPAdes, on several thousand small data sets generated with CAMISIM.
conclusionsCAMISIM can simulate a wide variety of microbial communities and metagenome data sets together with standards of truth for method evaluation. All data sets and the software are freely available at https://github.com/CAMI-challenge/CAMISIM.
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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.