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rnftools

RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.

https://github.com/karel-brinda/rnftools

Science Score: 33.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 9 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    2 of 5 committers (40.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.0%) to scientific vocabulary

Keywords

bioinformatics mapper-evaluation ngs ngs-format read-simulation
Last synced: 10 months ago · JSON representation

Repository

RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.

Basic Info
Statistics
  • Stars: 14
  • Watchers: 3
  • Forks: 5
  • Open Issues: 26
  • Releases: 0
Topics
bioinformatics mapper-evaluation ngs ngs-format read-simulation
Created over 11 years ago · Last pushed over 7 years ago
Metadata Files
Readme License

README.rst 

RNFtools
========

.. image:: https://travis-ci.org/karel-brinda/rnftools.svg?branch=master
	:target: https://travis-ci.org/karel-brinda/rnftools

.. image:: https://readthedocs.org/projects/rnftools/badge/?version=latest
	:target: http://rnftools.rtfd.org

.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square
	:target: https://anaconda.org/bioconda/rnftools

.. image:: https://badge.fury.io/py/RNFtools.svg
	:target: https://badge.fury.io/py/RNFtools

.. image:: https://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbtv524-brightgreen.svg
	:target: http://dx.doi.org/10.1093/bioinformatics/btv524

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1066626.svg
	:target: https://doi.org/10.5281/zenodo.1066626

**Read Naming Format** is a generic format for assigning
read names with encoded information about original positions.
**RNFtools** is an associated
software package which can:

* simulate RNF-compliant reads using a wide class of integrated read simulators (Art, DwgSim, Mason, WgSim, etc.), either from a single genome (i.e., a whole genome sequencing) or multiple genomes (i.e., a metagenomic simulation);
* evaluate mappers using RNF reads;
* convert non-RNF simulated reads to RNF (e.g., from SAM format);
* transform genomic coordinates of RNF reads between different coordinate systems (using chain LiftOver format).

Links
-----

**Web of the project:** http://karel-brinda.github.io/rnftools/

**RNF specification:** http://karel-brinda.github.io/rnf-spec/

**Documentation:** http://rnftools.rtfd.org

**Installation:** http://rnftools.readthedocs.org/en/latest/tutorial/00_installation.html

**Examples of usage:** http://github.com/karel-brinda/rnftools/tree/master/examples/01_tutorial

**Publication:** http://dx.doi.org/10.1093/bioinformatics/btv524

Owner

  • Name: Karel Břinda
  • Login: karel-brinda
  • Kind: user
  • Location: Rennes, France
  • Company: Inria/IRISA Rennes

Bioinformatics, Algorithms, Genomics, Pathogens, Rapid Diagnostics, and Antibiotic Resistance

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 494
  • Total Committers: 5
  • Avg Commits per committer: 98.8
  • Development Distribution Score (DDS): 0.053
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Karel Břinda k****a@g****m 468
Karel Břinda k****a@h****u 14
astewart-twist a****t@t****m 8
Karel Břinda k****a@u****r 3
The Gitter Badger b****r@g****m 1
Committer Domains (Top 20 + Academic)
gitter.im: 1 univ-mlv.fr: 1 twistbioscience.com: 1 hsph.harvard.edu: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 46
  • Total pull requests: 31
  • Average time to close issues: 3 months
  • Average time to close pull requests: 8 days
  • Total issue authors: 8
  • Total pull request authors: 4
  • Average comments per issue: 1.2
  • Average comments per pull request: 0.03
  • Merged pull requests: 28
  • 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
View more stats
Top Authors
Issue Authors
  • karel-brinda (30)
  • simonepignotti (4)
  • RSherman15 (3)
  • astewart-twist (3)
  • rsuchecki (2)
  • sibyllewohlgemuth (2)
  • zihhuafang (1)
  • alperyilmaz (1)
Pull Request Authors
  • karel-brinda (27)
  • gitter-badger (2)
  • astewart-twist (1)
  • simonepignotti (1)
Top Labels
Issue Labels
bug (17) enhancement (10) feature-request (4) question (1) wontfix (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 24 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 2
    (may contain duplicates)
  • Total versions: 20
  • Total maintainers: 1
pypi.org: rnftools

RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.

  • Versions: 19
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 17 Last month
Rankings
Dependent packages count: 10.0%
Forks count: 13.3%
Stargazers count: 15.2%
Dependent repos count: 21.7%
Average: 22.7%
Downloads: 53.4%
Maintainers (1)
karel.brinda
Last synced: 11 months ago
pypi.org: pyconfdict

Python configuration dictionary

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 7 Last month
Rankings
Dependent packages count: 10.1%
Forks count: 13.3%
Stargazers count: 15.3%
Dependent repos count: 21.6%
Average: 29.5%
Downloads: 87.3%
Maintainers (1)
karel.brinda
Last synced: 11 months ago

Dependencies

requirements.txt pypi
  • argparse *
  • beautifulsoup4 *
  • pyfaidx *
  • pysam *
  • snakemake *
  • svg42pdf >=0.1.1
setup.py pypi
  • argparse *
  • beautifulsoup4 *
  • pyfaidx *
  • pysam *
  • snakemake *
  • svg42pdf >=0.1.1
  • termcolor *