Mothur处理454测序流程和命令

454测序返回的结果是sff格式的文件

#sffinfo(sff=test.sff,flow=T)

#trim and bin sequences in flowgram
#trim.flows(flow=test.flow, oligos=test.oligos,bdiffs=0,pdiffs=1,processors=2)

#denoise to remove sequencing errors, create fasta and qual files
#shhh.flows(file=test.flow.files, processors=2)

#bin by barcode, trim fasta files, remove low quality sequence
#trim.seqs(fasta=test.shhh.fasta, name=test.shhh.names, oligos=test.oligos,flip=T,minlength=200,maxlength=500,maxambig=0,maxhomop=8,bdiffs=0,pdiffs=1,processors=2)

#remove redundant sequences
#unique.seqs(fasta=test.shhh.trim.fasta, name=test.shhh.trim.names)

#align sequences to template 16S rRNA gene
#align.seqs(fasta=test.shhh.trim.unique.fasta, reference=silva.bacteria/silva.bacteria.fasta, processors=2)

#summarize results so far
#summary.seqs(fasta=test.shhh.trim.unique.align, name=test.shhh.trim.names)

#determine clear-span region
#screen.seqs(fasta=test.shhh.trim.unique.align, name=test.shhh.trim.names, group=test.shhh.groups, end=6333, optimize=start, criteria=85, processors=2)

#remove sequences and cut alignment to clear span region
#filter.seqs(fasta=test.shhh.trim.unique.good.align, vertical=T, trump=., processors=2)

#remove redundant sequences
#unique.seqs(fasta=test.shhh.trim.unique.good.filter.fasta, name=test.shhh.trim.good.names)

#pre cluster sequences
#pre.cluster(fasta=test.shhh.trim.unique.good.filter.unique.fasta, name=test.shhh.trim.unique.good.filter.names, group=test.shhh.good.groups, diffs=2)

#run ClimeraSlayer to identify potential chimeras
#chimera.uchime(fasta=test.shhh.trim.unique.good.filter.unique.precluster.fasta, name=test.shhh.trim.unique.good.filter.unique.precluster.names, group=test.shhh.good.groups, processors=2)

#remove chimeras identified by ChimeraSlayer
#remove.seqs(accnos=test.shhh.trim.unique.good.filter.unique.precluster.uchime.accnos, fasta=test.shhh.trim.unique.good.filter.unique.precluster.fasta, name=test.shhh.trim.unique.good.filter.unique.precluster.names, group=test.shhh.good.groups)

参考资料：

http://shuixia100.weebly.com/1/post/2011/12/mothur-tutorial-2_analysis-example.html

http://www.microbiota.org/cgi-bin/tmp/mothur.cgi

https://wiki.hpcc.msu.edu/display/Bioinfo/Denoising+454+Data+with+Mothur

http://fasta.bioch.virginia.edu/cshl/metag/preprocess.html

http://fasta.bioch.virginia.edu/cshl/metag/meta_work1.html

http://prezi.com/rj6v76pnwkn0/introduction-to-mothur/

http://prezi.com/or6kaxsxafy0/mothur-part-2/

http://prezi.com/opyoremqjdyf/aligning-in-mothur-part-3/

原文来自：http://www.douban.com/note/258493418/