Mothur Linux上使用

一、安装

下载 http://www.mothur.org/wiki/Download_mothur， 我下载的是中间那个，但不知道最后一个的readline是干嘛的，有高手可以指点下。

下载后得到压缩文件Mothur_cen_64.zip，上传到服务器，解压：unzip Mothur_cen_64.zip，得到文件夹mothur，为了方便使用，可以将该文件夹的路径添加到环境变量中（编辑.bashrc文件）。

二、运行方式

1、Interactive mode 交互式

在terminal输入mothur进入交互式界面，

mothur >
mothur > align.seqs(help)
mothur > quit

2、Batch mode 批量运行模式

http://www.mothur.org/wiki/Batch_mode

把命令写到一个文件中batchfile

--------------------------------batchfile--------------------------------------
cluster(phylip=98_sq_phylip_amazon.dist, cutoff=0.1)
collect.single()
rarefaction.single() 
--------------------------------------------------------------------------------

运行：

../mothur/mothur batchfile

3、Command line mode 命令行模式

http://www.mothur.org/wiki/Command_line_mode

mothur "#read.dist(phylip=98_sq_phylip_amazon.dist, cutoff=0.1); cluster(); collect.single()"

命令间用分号分隔，所有的命令用双引号括起来，且括号内的命令以#号开头

三、Analysis examples

http://www.mothur.org/wiki/Analysis_examples

1、MiSeq SOP （standard operating procedure）http://www.mothur.org/wiki/MiSeq_SOP

（1）paire end根据overlap合并

首先做一个文件包含如下内容

--------------------------------stability.files-----------------------------
F3D0 F3D0_S188_L001_R1_001.fastq F3D0_S188_L001_R2_001.fastq
F3D141 F3D141_S207_L001_R1_001.fastq F3D141_S207_L001_R2_001.fastq
F3D142 F3D142_S208_L001_R1_001.fastq F3D142_S208_L001_R2_001.fastq
F3D143 F3D143_S209_L001_R1_001.fastq F3D143_S209_L001_R2_001.fastq
F3D144 F3D144_S210_L001_R1_001.fastq F3D144_S210_L001_R2_001.fastq
F3D145 F3D145_S211_L001_R1_001.fastq F3D145_S211_L001_R2_001.fastq
F3D146 F3D146_S212_L001_R1_001.fastq F3D146_S212_L001_R2_001.fastq
F3D147 F3D147_S213_L001_R1_001.fastq F3D147_S213_L001_R2_001.fastq
F3D148 F3D148_S214_L001_R1_001.fastq F3D148_S214_L001_R2_001.fastq
F3D149 F3D149_S215_L001_R1_001.fastq F3D149_S215_L001_R2_001.fastq
F3D150 F3D150_S216_L001_R1_001.fastq F3D150_S216_L001_R2_001.fastq
F3D1 F3D1_S189_L001_R1_001.fastq F3D1_S189_L001_R2_001.fastq
F3D2 F3D2_S190_L001_R1_001.fastq F3D2_S190_L001_R2_001.fastq
F3D3 F3D3_S191_L001_R1_001.fastq F3D3_S191_L001_R2_001.fastq
F3D5 F3D5_S193_L001_R1_001.fastq F3D5_S193_L001_R2_001.fastq
F3D6 F3D6_S194_L001_R1_001.fastq F3D6_S194_L001_R2_001.fastq
F3D7 F3D7_S195_L001_R1_001.fastq F3D7_S195_L001_R2_001.fastq
F3D8 F3D8_S196_L001_R1_001.fastq F3D8_S196_L001_R2_001.fastq
F3D9 F3D9_S197_L001_R1_001.fastq F3D9_S197_L001_R2_001.fastq
Mock Mock_S280_L001_R1_001.fastq Mock_S280_L001_R2_001.fastq
-----------------------------------------------------------------------------

mothur "#make.contigs(file=stability.files, processors=4)"

程序运行时需要调用libreadline.so.6，#很重要的，不要遗漏。该程序运行时需要调用libreadline.so.6动态链接库。

查看merge后reads的统计信息:

summary.seqs(fasta=stability.trim.contigs.fasta)

对merge后的reads进行过滤：

screen.seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups, maxambig=0, maxlength=275)

or

screen.seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups, summary=stability.trim.contigs.summary, maxambig=0, maxlength=275) #Faster than upper cmd

查看当前的有效对象：

get.current()
unique.seqs(fasta=stability.trim.contigs.good.fasta)

原文来自：http://liuwei441005.blog.163.com/blog/static/135705811201453094227246

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