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:

A full documentation with tutorials is available on http://rnftools.rtfd.org. Source codes of RNFtools are available in its GitHub repository.


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 rnftools liftover is mandatory.
17 September 2015 Version 0.2.1. A new subcommand rnftools liftover for LiftOvering coordinates in read names.
31 August 2015 Our paper was accepted to Bioinformatics.
9 July 2015 Version 0.2.0b. List of changes: For a list of all differences, see GitHub diff.
23 April 2015 Version 0.1.1. Support for Mason in MIShmash.
19 March 2015 Version 0.1.0. First release of RNFtools.

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