最近有点好奇,仅次于qiime的Mothur,用起来感觉如何,于是决定尝试下。虽然qiime还没有学会学透,但人活着就要折腾嘛,否则与咸鱼有什么区别,哈哈。
1.下载地址
Github项目地址–https://github.com/mothur/mothur
软件下载地址:https://github.com/mothur/mothur/releases/download/v1.40.5/Mothur.win_64.zip
p.s.这次决定用win10试试,我把thinkpad-额31上的12G内存分了4g给另一台电脑联想C2030,8g内存分析扩增子数据应该ok了。
2.安装和使用
安装就很简单了,解压到一个文件夹就哦了,然后,双击mothur.exe,竟然跳出一个cmd窗口,挺好的,门槛较低。
2.下面学习一下使用
2.1 下载示例数据
有两个版本,一个分好的,另一个是原始文件。
分好的样本数据:https://www.mothur.org/w/images/d/d6/MiSeqSOPData.zip
解压得到21对PEfastq数据,放在mothur程序文件夹。
原始文件:http://www.mothur.org/MiSeqDevelopmentData/StabilityNoMetaG.tar
解压得到362对PEfastq数据
make.file命令生成stability.files,这个应该是文件列表文件吧。
02 | make . file (inputdir=MiSeq_SOP, type =fastq, prefix=stability) |
04 | make .contigs( file =stability.files, processors=4) |
06 | summary.seqs(fasta=stability.trim.contigs.fasta) |
08 | screen .seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs. groups , maxambig=0, maxlength=275) |
09 | screen .seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs. groups , summary=stability.trim.contigs.summary, maxambig=0, maxlength=275) |
12 | Current RAM usage: 3.40499 Gigabytes. Total Ram: 7.88905 Gigabytes. |
14 | Current files saved by mothur: |
15 | accnos=MiSeq_SOP\stability.trim.contigs.bad.accnos |
16 | fasta=MiSeq_SOP\stability.trim.contigs.good.unique.fasta |
17 | group=MiSeq_SOP\stability.contigs.good. groups |
18 | name=MiSeq_SOP\stability.trim.contigs.good.names |
19 | qfile=MiSeq_SOP\stability.trim.contigs.qual |
20 | contigsreport=MiSeq_SOP\stability.contigs.report |
21 | count=MiSeq_SOP\stability.trim.contigs.good.count_table |
23 | summary=MiSeq_SOP\stability.trim.contigs.good.unique.summary |
24 | file =MiSeq_SOP\stability.files |
26 | Current input directory saved by mothur: MiSeq_SOP\ |
28 | Current default directory saved by mothur: D:\软件源文件\mothur\ |
30 | Current working directory: D:\软件源文件\mothur\ |
36 | unique.seqs(fasta=stability.trim.contigs.good.fasta) |
view source
02 | count.seqs(name=stability.trim.contigs.good.names, group=stability.contigs.good. groups ) |
04 | summary.seqs(count=stability.trim.contigs.good.count_table) |
06 | pcr.seqs(fasta=silva.bacteria.fasta, start=11894, end=25319, keepdots=F, processors=4) |
08 | rename. file (input=silva.bacteria.pcr.fasta, new=silva.v4.fasta) |
11 | summary.seqs(fasta=silva.v4.fasta) |
13 | align.seqs(fasta=stability.trim.contigs.good.unique.fasta, reference=silva.v4.fasta) |
15 | summary.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table)
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https://blog.sciencenet.cn/blog-623545-1123056.html
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