454测序返回的结果是sff格式的文件
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 | #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/
原文来自：http://www.douban.com/note/258493418/
