Cast your vote
You can rate an item by clicking the amount of stars they wish to award to this item.
When enough users have cast their vote on this item, the average rating will also be shown.
Your vote was cast
Thank you for your feedback
Thank you for your feedback
Lesker, Till R
DeMaere, Matthew Z
Darling, Aaron E
McHardy, Alice C
MetadataShow full item record
AbstractShotgun 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. We 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. CAMISIM 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.
CitationMicrobiome. 2019 Feb 8;7(1):17. doi: 10.1186/s40168-019-0633-6.
AffiliationBRICS, Braunschweiger Zentrum für Systembiologie, Rebenring 56,38106 Braunschweig, Germany.
The following license files are associated with this item:
- Creative Commons
Except where otherwise noted, this item's license is described as Attribution-NonCommercial-ShareAlike 4.0 International
- Evaluating de Novo Assembly and Binning Strategies for Time Series Drinking Water Metagenomes.
- Authors: Vosloo S, Huo L, Anderson CL, Dai Z, Sevillano M, Pinto A
- Issue date: 2021 Dec 22
- Practical evaluation of 11 de novo assemblers in metagenome assembly.
- Authors: Forouzan E, Shariati P, Mousavi Maleki MS, Karkhane AA, Yakhchali B
- Issue date: 2018 Aug
- Tamock: simulation of habitat-specific benchmark data in metagenomics.
- Authors: Gerner SM, Graf AB, Rattei T
- Issue date: 2021 May 1
- Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes.
- Authors: Papudeshi B, Haggerty JM, Doane M, Morris MM, Walsh K, Beattie DT, Pande D, Zaeri P, Silva GGZ, Thompson F, Edwards RA, Dinsdale EA
- Issue date: 2017 Nov 28
- Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit.
- Authors: Meyer F, Lesker TR, Koslicki D, Fritz A, Gurevich A, Darling AE, Sczyrba A, Bremges A, McHardy AC
- Issue date: 2021 Apr