  Aligning reads to a reference sequence is a fundamental step in numerous
bioinformatics pipelines. As a consequence, the sensitivity and precision of
the mapping tool, applied with certain parameters to certain data, can
critically affect the accuracy of produced results (e.g., in variant calling
applications). Therefore, there has been an increasing demand of methods for
comparing mappers and for measuring effects of their parameters.
  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. In
order to solve this obstacle, we have created a generic format RNF (Read Naming
Format) for assigning read names with encoded information about original
positions.
  Futhermore, we have developed an associated software package RNF containing
two principal components. MIShmash applies one of popular read simulating tools
(among DwgSim, Art, Mason, CuReSim etc.) and transforms the generated reads
into RNF format. LAVEnder evaluates then a given read mapper using simulated
reads in RNF format. A special attention is payed to mapping qualities that
serve for parametrization of ROC curves, and to evaluation of the effect of
read sample contamination.
