This repository holds the pipelines used in the TnpB project.
The pipelines are organized under subfolders.
tam_depletion_seq/: Identify the depleted TAM from sequencing reads.is605_annotation/: Annotate de novo IS605 elements from prokaryotic genomes.
- snakemake is needed for running the pipelines, and
- conda or mamba is needed to manage other software dependencies.
The pipelines are developed and tested under snakemake v7.14.0.
To use these pipelines, first clone this repository and install the dependencies. Detailed information on preparing input data and running the pipelines is available under the corresponding folder.
To cite this repo in publications, please use
Xiang, G., Li, Y., Sun, J. et al. Evolutionary mining and functional characterization of TnpB nucleases identify efficient miniature genome editors. Nat Biotechnol (2023). https://doi.org/10.1038/s41587-023-01857-x