Computer simulation reveals selection of library is related to read length of solexa sequencing in genome projects

In order to find the difference role of 200bp and 500bp libraries for genome assembly, a tool named SRSL was developed. It can simulate random solexa libraries based on reference sequence. Different depth and different read length of 200bp and 500bp libraries were produced by SRSL in four model species (rice, Arabidopsis, fruit fly and yeast). After assembling these sequences and calculating their contig N50 and scaffold N50, 200bp and 500bp libraries were compared for genome assembly. It is suggested that selection of 200bp or 500bp is closely related to read length of solexa sequence in the four genomes. When the read length of solexa is 50bp, it is shown 200bp and 500bp libraries should be selected together. When the read length of solexa is 100bp, it is sugguested 200bp library is not necessary to be sequenced. It is obviously different with past experience of solexa sequencing in genome projects. It would provide effective guide for solexa sequencing in the future genome projects.