https://github.com/karel-brinda/rnftools
RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.
https://github.com/karel-brinda/rnftools
bioinformatics mapper-evaluation ngs ngs-format read-simulation
Last synced: 8 months ago
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RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.
- Host: GitHub
- URL: https://github.com/karel-brinda/rnftools
- Owner: karel-brinda
- License: mit
- Created: 2015-02-27T12:33:40.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2018-11-18T23:48:21.000Z (almost 7 years ago)
- Last Synced: 2025-02-23T15:48:09.502Z (8 months ago)
- Topics: bioinformatics, mapper-evaluation, ngs, ngs-format, read-simulation
- Language: Python
- Homepage: http://karel-brinda.github.io/rnftools
- Size: 943 KB
- Stars: 14
- Watchers: 4
- Forks: 5
- Open Issues: 26
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
Awesome Lists containing this project
README
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