之前组装基因组一直用另外一个软件:SPAdes,组装效果还不错,但是IDBA的大名早就听说过,所以趁着这次刚那个两个菌的数据,分别用这两个软件组装一下,对比一下效果,在SPAdes的网站上面看到过几个组装软件的对比图,毫无疑问,SPAdes排第一,但是IDBA能排第二,说明IDBA的组装效果还可以。
一,使用说明
安装
If you use the
release package.
Exract the package, then use make to compile the source
code.
$ ./configure
$ make
Introduction
IDBA is the basic iterative de Bruijn graph assembler for
second-generation sequencing reads.
主要的部分分为以下三个:
IDBA-UD, an extension of IDBA, is designed to
utilize paired-end reads to assemble low-depth regions and use
progressive depth on contigs to reduce errors in high-depth
regions. It is a generic purpose assembler and epspacially
good for single-cell and metagenomic
sequencing data.
IDBA-Hybrid is another up