reper
reper: Genome-wide identification, classification and quantification of repetitive elements without an assembled genome - Published in JOSS (2018)
Science Score: 95.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 1 DOI reference(s) in JOSS metadata -
✓Academic publication links
Links to: joss.theoj.org, zenodo.org -
✓Committers with academic emails
2 of 3 committers (66.7%) from academic institutions -
○Institutional organization owner
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✓JOSS paper metadata
Published in Journal of Open Source Software
Repository
reper - Genome-wide identification, classification and quantification of repetitive elements without an assembled genome
Basic Info
- Host: GitHub
- Owner: nterhoeven
- License: mit
- Language: TeX
- Default Branch: master
- Homepage: https://github.com/nterhoeven/reper/wiki
- Size: 4.19 MB
Statistics
- Stars: 2
- Watchers: 3
- Forks: 2
- Open Issues: 1
- Releases: 2
Metadata Files
README.md
reper - Genome-wide identification, classification and quantification of repetitive elements without an assembled genome
What is reper?
reper is a pipeline to detect repetitive sequences in genome sequencing data. The detection is based on kmer frequencies and does not rely on a genome assembly. This allows an analysis of repeat sequences of organisms with large and repeat rich genomes (especially plants). For a detailed explanation of the pipeline, see the reper wiki.
How do I get reper?
reper is available as Docker container, Singularity image or can be installed manually. Please visit the reper wiki installation page for detailed explanations.
How do I run reper?
Running reper is very easy. You just need to adjust the config file and start reper with reper kmerCount.
A detailed explanation of the available commands is given in the usage page of the reper wiki.
Or you can take a look at the Tutorial and learn how to analyze the
repeat content of the sugar beet using reper.
How can I contribute?
Contribution to reper is always appreciated. Please submit any bugs, feature requests and similar via the github issue tracker. If you want to contribute code, feel free to fork this repository and/or open a pull request.
License and Citation
reper is placed under the MIT License.
Owner
- Login: nterhoeven
- Kind: user
- Repositories: 5
- Profile: https://github.com/nterhoeven
JOSS Publication
reper: Genome-wide identification, classification and quantification of repetitive elements without an assembled genome
Authors
Center for Computational and Thoeretical Biology, Universität Würzburg, Lehrstuhl für Bioinformatik, Universität Würzburg
Center for Computational and Thoeretical Biology, Universität Würzburg, Lehrstuhl für Bioinformatik, Universität Würzburg
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology
Editor
Melissa Gymrek
Tags
repeats transposons kmer pipeline repeat landscape NGSCodeMeta (codemeta.json)
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"@id": "https://orcid.org/0000-0002-8669-0000",
"@type": "Person",
"email": "niklas.terhoeven@uni-wuerzburg.de",
"name": "Niklas Terhoeven",
"affiliation": "Center for Computational and Theoretical Biology, Universität Würzburg"
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"@type": "Person",
"email": "Joerg.Schultz@biozentrum.uni-wuerzburg.de",
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"@type": "Person",
"email": "thackl@mit.edu",
"name": "Thomas Hackl",
"affiliation": "Department of Civil and Environmental Engineering, Massachusetts Institute of Technology"
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"identifier": "https://doi.org/10.5281/zenodo.1123479",
"codeRepository": "https://github.com/nterhoeven/reper",
"datePublished": "2017-12-21",
"dateModified": "2017-12-21",
"dateCreated": "2017-12-21",
"description": "reper - find, classify and quantify repeats without a genome assembly",
"keywords": "NGS, repeats, transposons, genome",
"license": "MIT",
"title": "reper",
"version": "v1.0.0"
}GitHub Events
Total
Last Year
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Niklas Terhoeven | n****n@u****e | 89 |
| Frank Förster | f****r@i****e | 38 |
| Arfon Smith | a****n | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 5
- Total pull requests: 7
- Average time to close issues: about 17 hours
- Average time to close pull requests: about 1 hour
- Total issue authors: 4
- Total pull request authors: 3
- Average comments per issue: 3.8
- Average comments per pull request: 0.29
- Merged pull requests: 7
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- greatfireball (2)
- dabitz (1)
- davidecarlson (1)
- nterhoeven (1)
Pull Request Authors
- nterhoeven (5)
- arfon (1)
- greatfireball (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- ubuntu 16.04 build