Read Naming Format and RNFtools
RNF
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
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).
News
| 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:
|
| 23 Apr 2015 | Version 0.1.1. Support for Mason in MIShmash. |
| 19 Mar 2015 | Version 0.1.0. The 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.