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

RNFtools

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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