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用罗氏454测序得到的序列用newbler拼接的效果最好，而用短序列拼接软件velvet拼接效果很差，所以不能将454的原始reads和Illumina产生的reads合到一起后用velvet进行拼接。在用newbler和velvet分别拼接454和Illumina的reads得到contigs之后，我们就需要将两者的contig再合并起来，得到更好的拼接结果。这里就介绍一个简单易用的软件minimus2。

minimus2是amos拼接软件包里面的一个组件，它的功能就是将两组contig进行合并，延伸contig的长度，减少contig的数量。Amos是A Modular, Open-Source whole genome assembler的缩写，致力于打造成一个拼接软件的基础软件系统。minimus2用的是基于nucmer overlap检测的算法，速度上比Smith-Waterman hash-overlap的算法要快，下面就介绍一下用法。

首先当然是下载amos软件包进行安装，下载地址为：http://sourceforge.net/projects/amos/files/

安装啥的就不说了，根据说明来就行。安装完成之后，minimus2软件位于amos安装文件夹下的bin里面。在运行minimus2之前首先要准备好文件，比如现在有s1.fa和s2.fa两组包含contig的文件，首先要知道里面包含的contig数目，针对fasta格式，用

grep -c "^>" s1.fa s2.fa  命令得到，比如分别为100和200个contig。

然后用cat命令合并到一个文件：

cat s1.fa s2.fa >s1_s2.fa

再用amos里面的另一个软件toAmos转换成Amos格式，这个软件也位于bin文件夹下面

./toAmos -s s1_s2.fa -o s1_s2.afg
这里的-s是指输入的为fasta格式。

然后就可以运行minimus2了

minimus2的运行参数为：

 minimus2 prefix  \
   -D REFCOUNT=n  \  # Number of sequences is the first set
   -D OVERLAP=n   \  # Minimum overlap (Default 40bp)
   -D CONSERR=f   \  # Maximum consensus error (0..1) (Def 0.06)
   -D MINID=n     \  # Minimum overlap %id for align. (Def 94)
   -D MAXTRIM=n      # Maximum sequence trimming length (Def 20bp)
最简单的命令为：
./minimus2 s1_s2 -D REFCOUNT=100

这里只要告诉文件名（不要后缀）和作为参考序列的第一组contig的数目就可以了。会生成一堆以s1_s2开头的文件，其中s1_s2.fasta就是合并之后得到的contig文件。

大功告成！

刚才闲逛发现了这篇被多家博客转载的文章，来自于SEQanswer，总结地比较全面，不过已经比较老了，随便看看~

Integrated solutions
* CLCbio Genomics Workbench – de novo and reference assembly of Sanger, Roche FLX, Illumina, Helicos, and SOLiD data. Commercial next-gen-seq software that extends the CLCbio Main Workbench software. Includes SNP detection, CHiP-seq, browser and other features. Commercial. Windows, Mac OS X and Linux.
* Galaxy – Galaxy = interactive and reproducible genomics. A job webportal.
* Genomatix – Integrated Solutions for Next Generation Sequencing data analysis.
* JMP Genomics – Next gen visualization and statistics tool from SAS. They are working with NCGR to refine this tool and produce others.
* NextGENe – de novo and reference assembly of Illumina, SOLiD and Roche FLX data. Uses a novel Condensation Assembly Tool approach where reads are joined via “anchors” into mini-contigs before assembly. Includes SNP detection, CHiP-seq, browser and other features. Commercial. Win or MacOS.
* SeqMan Genome Analyser – Software for Next Generation sequence assembly of Illumina, Roche FLX and Sanger data integrating with Lasergene Sequence Analysis software for additional analysis and visualization capabilities. Can use a hybrid templated/de novo approach. Commercial. Win or Mac OS X.
* SHORE – SHORE, for Short Read, is a mapping and analysis pipeline for short DNA sequences produced on a Illumina Genome Analyzer. A suite created by the 1001 Genomes project. Source for POSIX.
* SlimSearch – Fledgling commercial product. Continue reading “应用于第二代测序技术的生物信息学工具[zz]”