Whole-genome sequence assembly for mammalian genomes: Arachne 2
Whole-genome sequence assembly for mammalian genomes: Arachne 2
复制标题
DOI：
10.1101/gr.828403
复制
发表时间：
2003-01-01
期刊：
影响因子：
7
通讯作者：
Lander, ES
中科院分区：
文献类型：
--
作者：
Jaffe, DB;Butler, J;Lander, ES
我们之前描述了全基因组组装程序Arachne，展示了中小型基因组模拟数据的组装结果。在此我们介绍对该程序的算法调整，使其能够组装哺乳动物大小的基因组，并改进较小基因组的组装。在为期六个月的开发过程中，同时对小鼠基因组的组装进行了三项主要更改：（1）利用多种标准对重叠群（支架）进行反复拆分和重新连接，长度（N50）增加了64倍，并且明显消除了所有全局性错误连接；（2）通过插入读段（部分或完全地）填补重叠群中重叠群之间的间隙，这是根据重叠群内的配对情况提出的，使N50重叠群长度增加了50%；（3）内存使用量减少了四分之三。该小鼠组装的结果及其分析在（小鼠基因组测序联盟2002年）中有描述。
We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes. Three principal changes were simultaneously made and applied to the assembly of the mouse genome, during a six-month period of development: (1) Supercontigs (scaffolds) were iteratively broken and rejoined using several criteria, yielding a 64-fold increase in length (N50), and apparent elimination of all global misjoins; (2) gaps between contigs in supercontigs were filled (partially or completely) by insertion of reads, as suggested by pairing within the supercontig, increasing the N50 contig length by 50%; (3) memory usage was reduced fourfold. The outcome of this mouse assembly and its analysis are described in (Mouse Genome Sequencing Consortium 2002).