GSR: Simulator - CAMISIM
Attribute | Value |
---|---|
Title | CAMISIM |
Short Description | Simulating metagenomes and microbial communities |
Long Description | CAMISIM is a software to model abundance distributions of microbial communities and to simulate corresponding shotgun metagenome datasets. It was mainly developed for the Critical Assessment of Metagenome Annotation (CAMI) challenge, but should be suitable for general use. Please don't hesitate to open a new issue if you run into problems or need help. |
Project Started | 2019 |
Last Release | 5 years, 2 months ago |
Homepage | https://github.com/CAMI-challenge/CAMISIM |
Citations | Fritz A, Hofmann P, Majda S, Dahms E, Dröge J, Fiedler J, Lesker TR, Belmann P, DeMaere MZ, Darling AE, et al., CAMISIM: simulating metagenomes and microbial communities., Microbiome, 02-08-2019 [ Abstract, cited in PMC ] |
GSR Certification | ✔ Accessibility |
Last evaluated | 10-28-2021 (876 days ago) |
Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | Sequencing Reads, |
Variations | Other, |
Simulation Method | Other, |
Input | |
Data Type | |
File format | Other, |
Output | |
Data Type | |
Sequencing Reads | Other, |
File Format | SAM or BAM, |
Sample Type | |
Phenotype | |
Trait Type | |
Determinants | |
Evolutionary Features | |
Demographic | |
Population Size Changes | |
Gene Flow | |
Spatiality | |
Life Cycle | |
Mating System | |
Fecundity | |
Natural Selection | |
Determinant | |
Models | |
Recombination | |
Mutation Models | |
Events Allowed | |
Other | |
Interface | |
Development | |
Tested Platforms | |
Language | Python, |
License | Other, |
GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used CAMISIM.
2023
Gabrielli M, Dai Z, Delafont V, Timmers PHA, van der Wielen PWJJ, Antonelli M, Pinto AJ, Identifying Eukaryotes and Factors Influencing Their Biogeography in Drinking Water Metagenomes., Environ Sci Technol, 03-07-2023 [Abstract]
Xu R, Rajeev S, Salvador LCM, The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection., PLoS One, 04-07-2023 [Abstract]