General Information
| Description | A general framework to evaluate NGS read mappers |
| Homepage | http://karel-brinda.github.io/rnftools |
Publications
RNF: a general framework to evaluate NGS read mappers
Motivation:
Read simulators combined with alignment evaluation tools provide the most straightforward way to evaluate and compare mappers. Simulation of reads is accompanied by information about their positions in the source genome. This information is then used to evaluate alignments produced by the mapper. Finally, reports containing statistics of successful read alignments are created.
In default of standards for encoding read origins, every evaluation tool has to be made explicitly compatible with the simulator used to generate reads.
Results:
To solve this obstacle, we have created a generic format Read Naming Format (R nf ) for assigning read names with encoded information about original positions. Futhermore, we have developed an associated software package R nf Tools containing two principal components. MIS hmash applies one of popular read simulating tools (among D wg S im , A rt , M ason , C u R e S im , etc.) and transforms the generated reads into R nf format. LAVE nder evaluates then a given read mapper using simulated reads in R nf format. A special attention is payed to mapping qualities that serve for parametrization of R oc curves, and to evaluation of the effect of read sample contamination.
Availability and implementation:
R nf Tools: http://karel-brinda.github.io/rnftools Spec. of R nf : http://karel-brinda.github.io/rnf-spec
Contact:
karel.brinda@univ-mlv.fr
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