Reads maps from next-generation sequencing (NGS) technology. RMAP was developed for mapping Illumina reads and has been used to map Roche/454 and ABI SOLiD reads. The software reads map with or without error probability information. It supports paired-end reads either as read sequences or using full quality-score information. RMAP performance was profiled using data from resequencing bacterial artificial chromosomes (BACs) with well-known genomic origin (hg18).