Science Score: 59.0%
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 5 DOI reference(s) in README -
✓Academic publication links
Links to: pubmed.ncbi, ncbi.nlm.nih.gov -
✓Committers with academic emails
10 of 19 committers (52.6%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.6%) to scientific vocabulary
Keywords
assembly
bioinformatics
metagenomics
microbial-genomes
microbiology
Keywords from Contributors
genome
bacteria
phylogenetics
Last synced: 6 months ago
·
JSON representation
Repository
Rapid comparison and dereplication of genomes
Basic Info
Statistics
- Stars: 300
- Watchers: 7
- Forks: 40
- Open Issues: 18
- Releases: 6
Topics
assembly
bioinformatics
metagenomics
microbial-genomes
microbiology
Created over 9 years ago
· Last pushed 9 months ago
Metadata Files
Readme
Changelog
README.md
dRep
dRep is a python program for rapidly comparing large numbers of genomes. dRep can also "de-replicate" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set.
Manual, installation instructions, and API are at available at ReadTheDocs
Publication is available at ISMEJ
Open source pre-print publication is available at bioRxiv
Installation with pip
$ pip install drep
Quick start
Genome comparison:
$ dRep compare output_directory -g path/to/genomes/*.fasta
Genome de-replication:
$ dRep dereplicate output_directory -g path/to/genomes/*.fasta
Make sure dependencies are properly installed:
$ dRep check_dependencies
Dependencies
Near Essential
- Mash - Makes primary clusters (v1.1.1 confirmed works)
- MUMmer - Performs default ANIm comparison method (v3.23 confirmed works)
Optional
- fastANI - A fast secondary clustering algorithm
- CheckM_ - Determines contamination and completeness of genomes (v1.0.7 confirmed works)
- gANI (aka ANIcalculator) - Performs gANI comparison method (v1.0 confirmed works)
- Prodigal - Used be both checkM and gANI (v2.6.3 confirmed works)
- NSimScan - Only needed for goANI algorithm (open source version of gANI)
Owner
- Name: Matt Olm
- Login: MrOlm
- Kind: user
- Location: San Francisco, CA
- Company: Stanford University
- Website: https://mrolm.github.io/
- Twitter: MattagenOlmics
- Repositories: 8
- Profile: https://github.com/MrOlm
Postdoc in Justin Sonnenburg's lab at Stanford
GitHub Events
Total
- Issues event: 61
- Watch event: 54
- Issue comment event: 110
- Push event: 4
- Pull request event: 3
- Fork event: 2
Last Year
- Issues event: 61
- Watch event: 54
- Issue comment event: 110
- Push event: 4
- Pull request event: 3
- Fork event: 2
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Matt Olm | m****m@b****u | 96 |
| Matt Olm | m****m@M****l | 76 |
| Matt Olm | m****m@g****m | 41 |
| Matt Olm | m****m@M****l | 23 |
| Tanaes | j****n@g****m | 3 |
| Matt Olm | m****m@a****u | 3 |
| Ben J Woodcroft | d****n@g****m | 2 |
| Valentyn Bezshapkin | 6****z | 2 |
| Mike Lee | l****d@u****u | 2 |
| Matt Olm | m****m@s****u | 2 |
| Matt Olm | m****m@a****u | 2 |
| Matt Olm | m****m@a****u | 2 |
| Asaf Peer | A****r@j****g | 1 |
| Matt Olm | m****m@a****u | 1 |
| Matt Olm | m****m@a****u | 1 |
| Matt Olm | m****m@a****u | 1 |
| Malte Rühlemann | m****n@g****m | 1 |
| Francisco Zorrilla | f****4@c****k | 1 |
| Bérénice Batut | b****t@g****m | 1 |
Committer Domains (Top 20 + Academic)
cam.ac.uk: 1
airbears2-10-142-18-109.airbears2.1918.berkeley.edu: 1
airbears2-10-142-16-84.airbears2.1918.berkeley.edu: 1
airbears2-10-142-16-62.airbears2.1918.berkeley.edu: 1
jax.org: 1
airbears2-10-142-16-79.airbears2.1918.berkeley.edu: 1
airbears2-10-142-17-76.airbears2.1918.berkeley.edu: 1
sr22-ac376befe7.stanford.edu: 1
usc.edu: 1
airbears2-10-142-16-78.airbears2.1918.berkeley.edu: 1
biotite.berkeley.edu: 1
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 173
- Total pull requests: 13
- Average time to close issues: about 1 month
- Average time to close pull requests: 2 days
- Total issue authors: 142
- Total pull request authors: 10
- Average comments per issue: 3.95
- Average comments per pull request: 0.62
- Merged pull requests: 8
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 39
- Pull requests: 4
- Average time to close issues: 14 days
- Average time to close pull requests: about 8 hours
- Issue authors: 32
- Pull request authors: 3
- Average comments per issue: 1.79
- Average comments per pull request: 0.25
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- B-1991-ing (5)
- SilasK (5)
- jianshu93 (3)
- Chandrasekaran-J (3)
- Wanli-HE (2)
- sleepvet (2)
- pengfeimm (2)
- mewu3 (2)
- aretchless (2)
- nick-youngblut (2)
- jdwinkler-lanzatech (2)
- aistBMRG (2)
- rrohwer (2)
- franciscozorrilla (2)
- luigallucci (2)
Pull Request Authors
- tanaes (3)
- wwood (2)
- ShriramHPatel (2)
- ParsaGhadermazi (2)
- rroutsong (2)
- MrOlm (2)
- aboffin (1)
- bebatut (1)
- franciscozorrilla (1)
- valentynbez (1)
Top Labels
Issue Labels
enhancement (8)
bug (5)
documentation (4)
Pull Request Labels
Packages
- Total packages: 2
-
Total downloads:
- pypi 258 last-month
-
Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 1
(may contain duplicates) - Total versions: 67
- Total maintainers: 2
pypi.org: drep
De-replication of microbial genomes assembled from multiple samples
- Homepage: https://github.com/MrOlm/drep
- Documentation: https://drep.readthedocs.io/
- License: MIT
-
Latest release: 3.6.2
published 10 months ago
Rankings
Stargazers count: 4.8%
Forks count: 6.8%
Dependent packages count: 10.0%
Average: 11.0%
Downloads: 11.9%
Dependent repos count: 21.7%
Maintainers (1)
Last synced:
7 months ago
spack.io: py-drep
dRep is a python program for rapidly comparing large numbers of genomes. dRep can also "de-replicate" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set.
- Homepage: https://github.com/MrOlm/drep
- License: []
-
Latest release: 3.4.2
published almost 3 years ago
Rankings
Dependent repos count: 0.0%
Stargazers count: 16.4%
Forks count: 18.6%
Average: 23.1%
Dependent packages count: 57.3%
Maintainers (1)
Last synced:
6 months ago
Dependencies
requirements.txt
pypi
- biopython *
- matplotlib *
- numpy *
- pandas *
- pytest *
- scikit-learn *
- seaborn *
setup.py
pypi
- biopython *
- matplotlib *
- numpy *
- pandas *
- pytest *
- scikit-learn *
- seaborn *
- tqdm *