Read Naming Format and RNFtools
RNF (Read Naming Format, specification) is a generic format for assigning names to simulated Next-Generation Sequencing (NGS) reads. It provides a unified way of encoding genomic coordinates of reads, no matter which specific sequencing technology is simulated or which read simulator employed. Altogether, it simplifies evaluation of read mappers and debugging of tools for NGS data.
RNFtools is an associated software package for RNF, which can:
- simulate RNF-compliant reads using a wide class of integrated read simulators (Art, DwgSim, Mason, WgSim, etc.);
- 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).
|21 June 2017||Version 0.3.1. Support for sequence extraction.|
|18 April 2017||Version 0.3.0. A major update of RNFtools. The SMBL library for compiling the used programs on-the-fly is replaced by BioConda.|
|3 October 2015||
Version 0.2.2. Genome ID for
|17 September 2015||
Version 0.2.1. A new subcommand
|31 August 2015||Our paper was accepted to Bioinformatics.|
|9 July 2015||
Version 0.2.0b. List of changes:
|23 April 2015||Version 0.1.1. Support for Mason in MIShmash.|
|19 March 2015||Version 0.1.0. First release of RNFtools.|
Publications and posters
- K. Břinda, V. Boeva, and G. Kucherov. RNF: a general framework to evaluate NGS read mappers. Bioinformatics, doi:10.1093/bioinformatics/btv524, 2015.
- K. Břinda, V. Boeva, and G. Kucherov. RNF: a method and tools to evaluate NGS read mappers. Poster on RECOMB 2015.