tnpb
Snakemake workflows for TAM depletion analysis and de novo IS605 annotation
Science Score: 57.0%
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✓CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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✓DOI references
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○Scientific vocabulary similarity
Low similarity (6.3%) to scientific vocabulary
Keywords
Repository
Snakemake workflows for TAM depletion analysis and de novo IS605 annotation
Basic Info
- Host: GitHub
- Owner: Zhanglab-IOZ
- License: mit
- Language: Python
- Default Branch: main
- Homepage: http://zhanglab.ioz.ac.cn/
- Size: 36.1 KB
Statistics
- Stars: 4
- Watchers: 1
- Forks: 3
- Open Issues: 0
- Releases: 1
Topics
Metadata Files
README.md
This repository holds the pipelines used in the TnpB project.
Content
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.
Dependencies
- 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.
Usage
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.
Citation
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
Owner
- Name: Zhanglab-IOZ
- Login: Zhanglab-IOZ
- Kind: organization
- Repositories: 3
- Profile: https://github.com/Zhanglab-IOZ
Citation (CITATION.cff)
cff-version: 1.2.0
message: Please cite this repository using the metadata from "preferred-citation".
authors:
- given-names: Yuanqing
family-names: Li
orcid: 'https://orcid.org/0000-0003-2083-4339'
affiliation: 'Institute of Zoology, CAS'
title: Snakemake workflows for TAM depletion analysis and de novo IS605 annotation
type: software
version: 1.0.0
doi: 10.5281/zenodo.7952678
date-released: 2023-05-20
repository-code: 'https://github.com/Zhanglab-IOZ/TnpB'
preferred-citation:
type: article
authors:
- {given-names: Guanghai, family-names: Xiang, orcid: 'https://orcid.org/0000-0002-3495-1862'}
- {given-names: Yuanqing, family-names: Li, orcid: 'https://orcid.org/0000-0003-2083-4339'}
- {given-names: Jing, family-names: Sun}
- {given-names: Yongyuan, family-names: Huo}
- {given-names: Shiwei, family-names: Cao}
- {given-names: Yuanwei, family-names: Cao}
- {given-names: Yanyan, family-names: Guo}
- {given-names: Ling, family-names: Yang}
- {given-names: Yujia, family-names: Cai}
- {given-names: Yong E., family-names: Zhang, orcid: 'https://orcid.org/0000-0003-3770-2383'}
- {given-names: Haoyi, family-names: Wang, orcid: 'https://orcid.org/0000-0003-2135-1769'}
year: 2023
month: 6
day: 29
title: Evolutionary mining and functional characterization of TnpB nucleases identify efficient miniature genome editors
journal: Nature Biotechnology
# issue: 1
# volume: 1
# start: 1 # First page number
# end: 10 # Last page number
doi: 10.1038/s41587-023-01857-x
GitHub Events
Total
- Issues event: 5
- Watch event: 3
- Issue comment event: 16
- Push event: 1
- Fork event: 1
Last Year
- Issues event: 5
- Watch event: 3
- Issue comment event: 16
- Push event: 1
- Fork event: 1