Science Score: 57.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
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○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.3%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
EzAAI - High Throughput Prokaryotic AAI Calculator
Basic Info
- Host: GitHub
- Owner: endixk
- License: gpl-3.0
- Language: Java
- Default Branch: main
- Homepage: https://endixk.github.io/ezaai
- Size: 97 MB
Statistics
- Stars: 44
- Watchers: 3
- Forks: 5
- Open Issues: 17
- Releases: 5
Topics
Metadata Files
README.md
EzAAI: High Throughput Prokaryotic AAI Calculator
EzAAI is a suite of workflows for improved AAI calculation performance along with the novel module that provides hierarchical clustering analysis and dendrogram representation.
Quick start with conda
~~~bash conda install -c bioconda ezaai ezaai -h ~~~
Build from source
Requirements
- Java 8+
- Maven 3+ ~~~bash git clone https://github.com/endixk/ezaai.git cd ezaai mvn clean compile assembly:single java -jar target/EzAAI-*.jar -h ~~~
Available modules
extract
- Extract protein database(s) from genome using Prodigal
~~~bash
ezaai extract -i
|Argument|Description|
|:-:|-----------------|
|-i|Input file or directory with prokaryotic genome sequence(s)|
|-o|Output file or directory|
calculate
- Calculate AAI value from protein databases using MMseqs2
~~~bash
ezaai calculate -i
|Argument|Description|
|:-:|-----------------|
|-i|First input DB / directory with DBs|
|-j|Second input DB / directory with DBs|
|-o|Output result file|
convert
- Convert CDS FASTA file into MMseqs2 database
~~~bash
ezaai convert -i
|Argument|Description|
|:-:|-----------------|
|-i|Input CDS profile (FASTA format)|
|-s|Sequence type of input file (nucl/prot)|
|-o|Output database|
cluster
- Hierarchical clustering of taxa with AAI values
~~~bash
ezaai cluster -i
|Argument|Description|
|:-:|-----------------|
|-i|Input EzAAI result file containing all-by-all pairwise AAI values|
|-o|Output result file|
Owner
- Name: Daniel DW Kim
- Login: endixk
- Kind: user
- Location: Seoul, Korea
- Company: Seoul National University
- Twitter: endix_k
- Repositories: 1
- Profile: https://github.com/endixk
Studying bioinformatics in @steineggerlab, SNU.
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Kim"
given-names: "Dongwook"
orcid: "https://orcid.org/0000-0001-7386-3163"
- family-names: "Park"
given-names: "Sein"
- family-names: "Chun"
given-names: "Jongsik"
orcid: "https://orcid.org/0000-0003-3385-5171"
title: "EzAAI - High Throughput Prokaryotic AAI Calculator"
version: 1.2.2
doi: 10.1007/s12275-021-1154-0
preferred-citation:
type: article
authors:
- family-names: "Kim"
given-names: "Dongwook"
orcid: "https://orcid.org/0000-0001-7386-3163"
- family-names: "Park"
given-names: "Sein"
- family-names: "Chun"
given-names: "Jongsik"
orcid: "https://orcid.org/0000-0003-3385-5171"
doi: 10.1007/s12275-021-1154-0
journal: "Journal of Microbiology"
title: "Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity"
issue: 59
volume: 5
start: 476
end: 480
year: 2021
GitHub Events
Total
- Create event: 1
- Release event: 1
- Issues event: 7
- Watch event: 8
- Issue comment event: 12
- Push event: 8
- Fork event: 2
Last Year
- Create event: 1
- Release event: 1
- Issues event: 7
- Watch event: 8
- Issue comment event: 12
- Push event: 8
- Fork event: 2
Committers
Last synced: 6 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| DW Kim | e****9@g****m | 37 |
| lebsnu | 4****u | 10 |
| Daniel DW Kim | 4****9 | 4 |
| Aaron Mussig | a****g@g****m | 2 |
| psi103706 | 4****6 | 1 |
| dependabot[bot] | 4****] | 1 |
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 25
- Total pull requests: 8
- Average time to close issues: 4 days
- Average time to close pull requests: 5 days
- Total issue authors: 24
- Total pull request authors: 3
- Average comments per issue: 2.0
- Average comments per pull request: 0.13
- Merged pull requests: 8
- Bot issues: 0
- Bot pull requests: 1
Past Year
- Issues: 6
- Pull requests: 1
- Average time to close issues: 8 days
- Average time to close pull requests: 1 minute
- Issue authors: 6
- Pull request authors: 1
- Average comments per issue: 0.5
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 1
Top Authors
Issue Authors
- bluegenes (2)
- beajorrin (1)
- carlodere (1)
- Ekie22 (1)
- lauraflows (1)
- caizhangbin (1)
- ak-watson (1)
- rihab-tech (1)
- AleksandarStan (1)
- cruizperez (1)
- zackhenny (1)
- 994422 (1)
- achenderson (1)
- shlomobl (1)
- neptuneyt (1)
Pull Request Authors
- endixk (6)
- dependabot[bot] (2)
- aaronmussig (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/checkout v3 composite
- actions/setup-java v3 composite
- commons-io:commons-io 2.11.0 compile
- com.googlecode.json-simple:json-simple 1.1
- org.biojava:biojava3-core 3.0