Comparative Scaffolding and Gap Closure Using Next Generation Sequencing

• Main Authors: Wang, Hsiaowen, 王筱文
• Other Authors: Huang, Yaoting
• Format: Others
• Language: en_US
• Published: 2011
• Online Access: http://ndltd.ncl.edu.tw/handle/34573992629587433153

碩士 === 國立中正大學 === 資訊工程研究所 === 99 === Next Generation Sequencing (NGS) technologies have been widely used to assemble the genomes of unstudied species in the biosphere. In practice, the assembled genomes are very fragmented due to the complexity of the genome and relatively short length of reads. In this thesis, we design and implement a comparative Scaffolding And Gap closure Assembler (called SAGA). By comparatively analyzing a related genome, SAGA carefully refines the boundary of each contig mapped on the related genome and links the contigs with no rearrangement events into scaffolds. For each gap within the scaffold, SAGA further used a jumping assembly approach to assemble isolated islands of reads in the gap, which overcomes the limitations of assembling low or no coverage regions. SAGA has been tested and compared with other methods using a variety of simulated and real data sets. The experimental results indicated that SAGA significantly produced a more contiguous genome with larger N50 compared with other programs. It is worth mentioning that SAGA is able to assist scaffolding the assembly using related genome with similarity as low as 80%. Compared with physical or optical map approaches, SAGA is very cost-effective toward the genome finishing.