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.


18 Nov 2018 RNFtools moved to http://rnftools.github.io
4 Jul 2017 Version 0.3.3. Support for CuReSim random mode.
21 Jun 2017 Version 0.3.2. Support for the vcf parameter in sequence DWGsim.
21 Jun 2017 Version 0.3.1. Support for sequence extraction.
18 Apr 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 Oct 2015 Version 0.2.2. Genome ID for rnftools liftover is mandatory.
17 Sep 2015 Version 0.2.1. A new subcommand rnftools liftover for LiftOvering coordinates in read names.
31 Aug 2015 Our paper was accepted to Bioinformatics.
9 Jul 2015 Version 0.2.0b. List of changes: For a list of all differences, see GitHub diff.
23 Apr 2015 Version 0.1.1. Support for Mason in MIShmash.
19 Mar 2015 Version 0.1.0. The first release of RNFtools.

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