Mapping short reads to a genome without using hash look-up table algorithm and Burrows Wheeler Transformation

Many new sequencing techniques have been proposed in the last few years. A number of tools have been developed for mapping short reads to the genome. However, these tools used the hash look-up table algorithm for reads or for the genome. With more and more reads sequenced and the length of reads increases; these tools will require huge memory usage and may be not practical for biologists and applications. Recently, new tools were designed to overcome this problem by using Burrows Wheeler Transformation. In this paper, we propose a program, FRESCO, without using hash look-up table algorithm and Burrows Wheeler Transformation. By well-designed techniques in FRESCO, the memory usage can be controlled by users. A case study of micro-RNAs (miRNAs) was applied into FRESCO and the results showed that FRESCO can only used 268MB memory and mapped reads to all of known miRNAs and 98.6% novel miRNAs candidates.