SOAPdenovo_Readme的认识.doc

Introduction SOAPdenovo is a novel short-read assembly method that can build a draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo是一种新型的short-read装配方法,可以建立一个de novo组装人l类大小的基因组草案。这个程序是为装配Illumina测序 short reads特别设计的。它以一种高效益的方式为建立参考序列和计算出精确的未知基因组创造了新的机会。 System Requirement SOAPdenovo aims for large plant and animal genomes, although it also works well on bacteria and fungi genomes. It runs on 64-bit Linux system with a minimum of 5G physical memory. For big genomes like human, about 150 GB memory would be required. SOAPdenovo虽然也能在细菌和真菌基因组也能很好的运行但它的目标是大的植物和动物的基因组。它运行在最小内存5G的64位Linux系统上。像人类的大基因组，大约需要150G内存。 Download Release 1.0 Only precompiled binary version available now. 只有预编译的二进制版本 Installation Download the SOAPdenovo tar package; 下载压缩包 Unpack it; 解压 There are one executable file “soapdenovo”, one demo configure file “example.contig” and this readme file. 有一个可执行文件soapdenovo，一个演示配置文件“example.contig”和这个readme文件。 How to use it 如何使用 Configuration file 配置文件 For big genome projects with deep sequencing, the data is usually organized as multiple read sequence files generated from multiple libraries. The configuration file tells the assembler where to find these files and the relevant information. “example.config” is an example of such a file. 对于深度测序的大的基因组项目，数据通常是多重函数库生成的多重read序列文件。配置文件告诉汇编如何寻找这些文件以及相关信息。“example.config”就是一个这样文件的例子。 The configuration file has a section for global information, and then multiple library sections. Right now only “max_rd_len” is included in the global information section. Any read longer than max_rd_len will be cut to this length. 这些配置文件有一个部分是总体信息，然后是多重文库部分。现在只有“max_rd_len”是包括在总体信息的部分。任何长于最大可读长度的read将被剪切到这个长度。 The library information and the information of sequencing data generated from the library should be organized in the cor