RNASIM: A simulation tool for transcriptome sequencing

DNA sequencing technology has played an important role on life sciences, especially Illumina's sequencer. It was used for more and more transcriptome projects. In this paper, we developed a tool named as RNASIM, which can simulate solexa transcriptome sequencing based on the reference sequences. The tool RNASIM can actually simulate random gene expression and insert size of library with normal distribution in solexa pair-end sequencing. In order to validate the tool, three times of experiments were simulated based on the reference Arabidopsis thaliana's transcripts and produced total reads' length of 1Gb, 2Gb and 4Gb. Simulated reads were assembled and compared with original reference sequences. There were respectively 19,704, 20,376 and 20,692 transcripts aligned to one assembled contig. And there were only 1,071(3.2%), 849(2.5%) and 778(2.3%) original transcripts were not found related contigs in three assembled transcripts. Others were assembled multiple copy because of alternative splicing or gene duplication.