一、安裝
下載 http://www./wiki/Download_mothur， 我下載的是中間那個，但不知道最后一個的readline是干嘛的，有高手可以指點下。
下載后得到壓縮文件Mothur_cen_64.zip，上傳到服務(wù)器，解壓：unzip Mothur_cen_64.zip，得到文件夾mothur，為了方便使用，可以將該文件夾的路徑添加到環(huán)境變量中（編輯.bashrc文件）。
二、運行方式
1、Interactive mode 交互式
在terminal輸入mothur進入交互式界面，
mothur >
mothur > align.seqs(help)
mothur > quit
2、Batch mode 批量運行模式
http://www./wiki/Batch_mode
把命令寫到一個文件中batchfile
--------------------------------batchfile--------------------------------------
cluster(phylip=98_sq_phylip_amazon.dist, cutoff=0.1)
collect.single()
rarefaction.single()
--------------------------------------------------------------------------------
運行：
../mothur/mothur batchfile
3、Command line mode 命令行模式
http://www./wiki/Command_line_mode
mothur "#read.dist(phylip=98_sq_phylip_amazon.dist, cutoff=0.1); cluster(); collect.single()"
命令間用分號分隔，所有的命令用雙引號括起來，且括號內(nèi)的命令以#號開頭
三、Analysis examples
http://www./wiki/Analysis_examples
1、MiSeq SOP （standard operating procedure）http://www./wiki/MiSeq_SOP
（1）paire end根據(jù)overlap合并
首先做一個文件包含如下內(nèi)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)"
程序運行時需要調(diào)用libreadline.so.6，#很重要的，不要遺漏。該程序運行時需要調(diào)用libreadline.so.6動態(tài)鏈接庫。
查看merge后reads的統(tǒng)計信息:
summary.seqs(fasta=stability.trim.contigs.fasta)
對merge后的reads進行過濾：
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
查看當前的有效對象：
get.current()
unique.seqs(fasta=stability.trim.contigs.good.fasta)
原文來自：http://liuwei441005.blog.163.com/blog/static/135705811201453094227246
