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SPAdes (St. Petersburg genome assembler)〔http://spades.bioinf.spbau.ru/release3.0.0/manual.html〕 is a genome assembly algorithm which was designed for single cell and multi-cells bacterial data sets. However, it might not be suitable for large genomes projects.〔 SPAdes works with Ion Torrent, PacBio and Illumina paired-end, mate-pairs and single reads.〔 Recently, SPAdes has been integrated into Galaxy pipelines by Guy Lionel and Philip Mabon.〔(Galaxy tool shed )〕 ==Background== Studying the genome of single cells will help to track changes that occur in DNA over time or associated with exposure to different conditions. Additionally, many projects such as Human Microbiome Project and antibiotics discovery would greatly benefit from Single-cell sequencing (SCS). SCS has an advantage over sequencing DNA extracted from large number of cells. The problem of averaging out the significant variations between cells can be overcome by using SCS. Experimental and computational technologies are being optimized to allow researchers to sequence single cells. For instance, amplification of DNA extracted from a single cell is one of the experimental challenges. To maximize the accuracy and quality of SCS, a uniform DNA amplification is needed. It was demonstrated that using multiple annealing and looping-based amplification cycles (MALBAC) for DNA amplification generates less biasness compared to polymerase chain reaction (PCR) or multiple displacement amplification (MDA).〔http://news.harvard.edu/gazette/story/2013/01/one-cell-is-all-you-need/〕 Furthermore, it has been recognized that the challenges facing SCS are computational rather than experimental. Currently available assembler, such as Velvet, String Graph Assembler (SGA) and EULER-SR, were not designed to handle SCS assembly.〔 Assembly of single cell data is difficult due to non-uniform read coverage, variation in insert length, high levels of sequencing errors and chimeric reads.〔 Therefore, the new algorithmic approach, SPAdes, was designed to address these issues. 抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』 ■ウィキペディアで「SPAdes (software)」の詳細全文を読む スポンサード リンク
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