Supporting data for "ANNOgesic: A Swiss army knife for the RNA-Seq based annotation of bacterial/archaeal genomes"
Dataset type: Software, Transcriptomic
Data released on July 17, 2018
Yu SH; Vogel J; Förstner KU (2018): Supporting data for "ANNOgesic: A Swiss army knife for the RNA-Seq based annotation of bacterial/archaeal genomes" GigaScience Database. https://doi.org/10.5524/100481
To understand the gene regulation of an organism of interest, a comprehensive genome annotation is essential. While some features, such as coding sequences, can be computationally predicted with high accuracy based purely on the genomic sequence, others, such as promoter elements or non-coding RNAs are harder to detect. RNA-Seq has proven to be an efficient method to identify these genomic features and to improve genome annotations. However, processing and integrating RNA-Seq data in order to generate high-resolution annotations is challenging, time consuming and requires numerous different steps. We have constructed a powerful and modular tool called ANNOgesic that provides the required analyses and simplifies RNA-Seq-based bacterial and archaeal genome annotation. It can integrate data from conventional RNA-Seq and dRNA-Seq, predicts and annotates numerous features, including small non-coding RNAs, with high precision. The software is available under an open source license (ISCL) at https://pypi.org/project/ANNOgesic/.
Additional details
Read the peer-reviewed publication(s):
- Yu, S.-H., Vogel, J., & Förstner, K. U. (2018). ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes. GigaScience, 7(9). https://doi.org/10.1093/gigascience/giy096 (PubMed:30169674)
Additional information:
https://github.com/Sung-Huan/ANNOgesic
https://pypi.org/project/ANNOgesic/
http://annogesic.readthedocs.io/en/latest/subcommands.html
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Table SettingsFile Name | Description | Sample ID | Data Type | File Format | Size | Release Date | File Attributes | Download |
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Readme | TEXT | 2.19 kB | 2018-07-02 | MD5 checksum: 7a954997f51b6dde89fee81287e43f95 |
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Archival copy of the GitHub repository https://github.com/Sung-Huan/ANNOgesic download 29-Jun-2018. ANNOgesic - A Swiss army knife for the RNA-Seq based annotation of bacterial/archaeal genomes | GitHub archive | archive | 655.90 kB | 2018-07-02 | RRID: SCR_016326 MD5 checksum: f5564ef8c9d18be8d2a942f33eeddc18 |
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Archival copy of software available from the PyPI repository https://pypi.org/project/ANNOgesic/ download 29-Jun-2018. ANNOgesic - A tool for bacterial/archaeal RNA-Seq based genome annotations | Software | TAR | 574.89 kB | 2018-07-02 | RRID: SCR_016326 MD5 checksum: 6104ed63fedc07295e3729b259f53eac |
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Archival copy of software available from the PyPI repository https://pypi.org/project/ANNOgesic/ download 29-Jun-2018. ANNOgesic - A tool for bacterial/archaeal RNA-Seq based genome annotations | Software | UNKNOWN | 299.77 kB | 2018-07-02 | RRID: SCR_016326 MD5 checksum: 771d5b1cbfe36fa3438baebd2fe71ba3 |
Funding body | Awardee | Award ID | Comments |
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Deutsche Forschungsgemeinschaft | J Vogel | CRC-TRR34 | Transregio 34 |
Code Ocean:
Date | Action |
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July 17, 2018 | Dataset publish |
July 24, 2018 | External Link added : https://doi.org/10.24433/CO.6eae18de-4c12-4245-86fc-e9a447d22c68 |
July 24, 2018 | External Link updated : CO.6eae18de-4c12-4245-86fc-e9a447d22c68 |
July 24, 2018 | External Link updated : |
July 24, 2018 | External Link updated : |
August 22, 2018 | Manuscript Link added : 10.1093/gigascience/giy096 |
November 11, 2022 | Manuscript Link updated : 10.1093/gigascience/giy096 |