Design And Implementation Of Whole Genome Shotgun Assembly System For Japan Schistosome

Shotgun method has remained the mainstay of genome sequence assembly for more than 20 years. The method is quite mature. But there are still many challenges in the practice whole genome shotgun assembly for large eukaryote genomes which contains lots of repeat sequences.First, the basic processes of shotgun sequencing and genome assembly are introduced. The main method involves obtaining random sequence reads from a genome, based on sequence overlap assembling them into contigs and determining their relative order on genome. Then we give a brief presentation about the background and practice of Japan Schistosome genome project. MIT's arachne is chosen as our assembler. Some problems about software transplant and data preparation are considered. Based on theoretic analysis and data simulation, we have found the main shortcomings of arachne.After that, according to the existent problem of arachne, we have developed a post-process scheme. The main idea is to combine or prolong arachne's contigs based on overlap and clone-end link information. The main steps of our post-process scheme are introduced, including detailed algorithms and results analysis.Finally, we discuss about what the ideal assembler should be, what kind of original reads data are effective and how to do in further research. As bioinformatics is a new and cross-discipline area, many relative biology, computer and math skills are still under developing. We give a prospective view of bioinformatics in the end.