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nvaulin committed Feb 19, 2024
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*Metagenomics* – key approach for biological community analysis. Many new tools appear regularly and their validation becomes the crucial challenge.


Here we come up with an artificial data generation tool `SAMOVAR` that aims aims to improve algorithms development and accelerate scientific discoveries.
Here we come up with an artificial data generation tool `SAMOVAR` that aims to improve algorithms development and accelerate scientific discoveries.
This pipeline takes the input phenotype or environment as a community property and technical parameters for NGS library to generate `fastq` files with Illumina reads. SAMOVAR performes additional bacteria selection based on a given *metabolite* or *metabolic pathways*. Overall, our pipeline consists of four steps:
- Core-bacterial set selection by given phenotype;
- Selection of additional bacteria species based on metabolites and metabolic pathways;
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### Citation
If you use these tool, please cite as:
- Vaulin N., Chechenina A., Ivanov. A, Ulyantsev V. SAMOVAR: a pipeline for *in silico* generation of metagenomic communities with given properties. Природа, 2023, 443, 27–28
- Chechenina A., Vaulin N., Ivanov. A, Ulyantsev V. Development of *in-silico* models of metagenomic communities with given properties and a pipeline for their generation. Bioinformatics institute 2022/23, 2023, 22-24
```bibtex
@article{samovar2023,
title={SAMOVAR: a pipeline for in silico generation of metagenomic communities with given properties},
author={Vaulin, N. and Chechenina, A. and Ivanov, A. and Ulyantsev, V.},
journal={Природа},
title={Development of in-silico models of metagenomic communities with given properties and a pipeline for their generation},
author={Chechenina, A. and Vaulin, N. and Ivanov, A. and Ulyantsev, V.},
journal={Bioinformatics institute 2022/23},
year={2023},
volume={443},
pages={27--28}
pages={22--24}
}
```

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