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transrate

Understand your transcriptome assembly

https://github.com/blahah/transrate

Science Score: 41.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 9 committers (11.1%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.3%) to scientific vocabulary

Keywords from Contributors

bioinformatics
Last synced: 10 months ago · JSON representation ·

Repository

Understand your transcriptome assembly

Basic Info
Statistics
  • Stars: 102
  • Watchers: 11
  • Forks: 35
  • Open Issues: 74
  • Releases: 14
Created almost 13 years ago · Last pushed over 2 years ago
Metadata Files
Readme License Citation

README.md

Transrate - understand your transcriptome assembly

Download latest binaries:
Need help? Chat to us live:

Development status

Gem Version Downloads Total Downloads Build Status Dependency Status Code Climate Coverage Status

This software is being actively developed. Please be aware that there may be bugs. If you find any, please report them on the issue tracker.

Citation

Transrate is academic software. If you use it for work leading to a publication, you should cite the paper.

Documentation

transrate is documented on the website.

Contributing

Interested in helping? Great! We particularly would like help with the following:

  • code review
  • documentation review
  • adding features that are already discussed and approved on the issue tracker
  • tackling bugs

For any of these, please just pick an appropriate issue on the tracker and make a pull request.

If you want to suggest, and maybe implement, a new feature, please suggest it on the tracker first. This allows us to give feedback on whether it makes sense given the scope of the software, and for the community to discuss requirements for the feature. Don't just implement the feature and make a pull request before dicussing it, because you'll probably find your PR waiting a very long time for review.

Owner

  • Name: Rik
  • Login: blahah
  • Kind: user
  • Location: Tigoni, Kenya
  • Company: @labdao

All my contributions on github issue trackers are placed in the public domain using the CC-Zero v1.0 (https://goo.gl/vUqlmV) dedication.

Citation (CITATION.md) 

TransRate is described in our paper: http://dx.doi.org/10.1101/gr.196469.115. 

To cite transrate in publications, please use:

## Plaintext

```
TransRate: reference free quality assessment of de-novo transcriptome assemblies (2016)
Richard D Smith-Unna, Chris Boursnell, Rob Patro, Julian M Hibberd, Steven Kelly.
Genome Research. doi: http://dx.doi.org/10.1101/gr.196469.115
```

## Bibtex 

```
@article{Smith-Unna01062016,
  author = {Smith-Unna, Richard and Boursnell, Chris and Patro, Rob and Hibberd, Julian and Kelly, Steven}, 
  title = {TransRate: reference free quality assessment of de novo transcriptome assemblies},
  year = {2016}, 
  doi = {10.1101/gr.196469.115}, 
  abstract ={TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies. Using only the sequenced reads and the assembly as input, we show multiple common artifacts of de novo transcriptome assembly can be readily detected. These include chimeras, structural errors, incomplete assembly and base errors. TransRate evaluates these errors to produce a diagnostic quality score for each contig and these contig scores are integrated to evaluate whole assemblies. Thus TransRate can be used for do novo assembly filtering and optimisation as well as comparison of assemblies generated using different methods from the same input reads. Applying the method to a dataset of 155 published de novo transcriptome assemblies we deconstruct the contribution that assembly method, read length, read quantity, and read quality make to the accuracy of de novo transcriptome assemblies and reveal that variance in the quality of the input data explains 43% of the variance in the quality of published de novo transcriptome assemblies. As TransRate is reference-free it is suitable for assessment of assemblies of all types of RNA, including assemblies of long non-coding RNA, rRNA, mRNA, and mixed RNA samples.}, 
  URL = {http://genome.cshlp.org/content/early/2016/06/01/gr.196469.115.abstract}, 
  eprint = {http://genome.cshlp.org/content/early/2016/06/01/gr.196469.115.full.pdf+html}, 
  journal = {Genome Research} 
}
```

## RIS

```
TY  - JOUR
A1  - Smith-Unna, Richard
A1  - Boursnell, Chris
A1  - Patro, Rob
A1  - Hibberd, Julian
A1  - Kelly, Steven
T1  - TransRate: reference free quality assessment of de novo transcriptome assemblies
Y1  - 2016/06/01 
JF  - Genome Research 
JO  - Genome Research 
N1  - 10.1101/gr.196469.115 
UR  - http://genome.cshlp.org/content/early/2016/06/01/gr.196469.115.abstract 
N2 - TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies. Using only the sequenced reads and the assembly as input, we show multiple common artifacts of de novo transcriptome assembly can be readily detected. These include chimeras, structural errors, incomplete assembly and base errors. TransRate evaluates these errors to produce a diagnostic quality score for each contig and these contig scores are integrated to evaluate whole assemblies. Thus TransRate can be used for do novo assembly filtering and optimisation as well as comparison of assemblies generated using different methods from the same input reads. Applying the method to a dataset of 155 published de novo transcriptome assemblies we deconstruct the contribution that assembly method, read length, read quantity, and read quality make to the accuracy of de novo transcriptome assemblies and reveal that variance in the quality of the input data explains 43% of the variance in the quality of published de novo transcriptome assemblies. As TransRate is reference-free it is suitable for assessment of assemblies of all types of RNA, including assemblies of long non-coding RNA, rRNA, mRNA, and mixed RNA samples. 
ER  -
```

GitHub Events

Total
  • Watch event: 2
  • Issue comment event: 3
Last Year
  • Watch event: 2
  • Issue comment event: 3

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 851
  • Total Committers: 9
  • Avg Commits per committer: 94.556
  • Development Distribution Score (DDS): 0.611
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Chris Boursnell c****l@g****m 331
Richard Smith-Unna r****4@g****m 292
Richard Smith r****5@c****k 220
Richard Smith-Unna r****k@f****o 3
The Gitter Badger b****r@g****m 1
Rory Kirchner r****r@g****m 1
Joshua Orvis j****s@g****m 1
vagrant v****t@p****) 1
Richard Smith-Unna r****5@X****l 1
Committer Domains (Top 20 + Academic)
precise64.(none): 1 gitter.im: 1 fathomlabs.io: 1 cam.ac.uk: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 97
  • Total pull requests: 7
  • Average time to close issues: 6 months
  • Average time to close pull requests: 5 days
  • Total issue authors: 64
  • Total pull request authors: 6
  • Average comments per issue: 3.1
  • Average comments per pull request: 0.29
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 minute
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • blahah (14)
  • macmanes (9)
  • ctb (4)
  • asan-emirsaleh (3)
  • KhudyakovLab (2)
  • VaneSGT (2)
  • RuiMMFaria (2)
  • abshah (2)
  • johnsolk (2)
  • manuelsmendoza (2)
  • jorvis (2)
  • lychen83 (1)
  • dcopetti (1)
  • lplough (1)
  • simonvh (1)
Pull Request Authors
  • pmomadeira (2)
  • IdoBar (2)
  • blahah (2)
  • macmanes (1)
  • gbrsales (1)
  • jorvis (1)
Top Labels
Issue Labels
enhancement (19) bug (6) documentation (6) good first issue (6) devops (5) can't reproduce (4) question (2) longterm (2) blocked (1) discussion (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • rubygems 78,769 total
  • Total dependent packages: 2
    (may contain duplicates)
  • Total dependent repositories: 5
    (may contain duplicates)
  • Total versions: 38
  • Total maintainers: 2
proxy.golang.org: github.com/blahah/transrate
  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 6.5%
Average: 6.7%
Dependent repos count: 7.0%
Last synced: 10 months ago
rubygems.org: transrate

a library and command-line tool for quality assessment of de-novo transcriptome assemblies

  • Versions: 31
  • Dependent Packages: 2
  • Dependent Repositories: 5
  • Downloads: 78,769 Total
Rankings
Forks count: 4.8%
Dependent packages count: 5.3%
Stargazers count: 5.5%
Average: 7.1%
Dependent repos count: 9.9%
Downloads: 10.2%
Maintainers (2)
Blahah cboursnell
Last synced: 10 months ago

Dependencies

transrate.gemspec rubygems
  • bindeps ~> 1.2, >= 1.2.1 development
  • coveralls ~> 0.7, >= 0.7.2 development
  • minitest ~> 5 development
  • minitest-reporters ~> 1, >= 1.0.17 development
  • rake ~> 10.3, >= 10.3.2 development
  • rake-compiler ~> 0.9, >= 0.9.2 development
  • shoulda ~> 3.5, >= 3.5.0 development
  • simplecov ~> 0.8, >= 0.8.2 development
  • test-unit ~> 3.0 development
  • bindeps ~> 1.2, >= 1.2.1
  • bio ~> 1.4, >= 1.4.3
  • colorize ~> 0.7, >= 0.7.7
  • crb-blast ~> 0.6, >= 0.6.4
  • trollop ~> 2.0, >= 2.0.0
  • yell ~> 2.0, >= 2.0.4
Gemfile rubygems