#pcr.seqs(fasta=silva.bacteria.fasta, start=11894, end=25319, keepdots=F) #system(mv silva.bacteria.pcr.fasta silva.v4.fasta) #change the name of the file from stability.files to whatever suits your study make.contigs(file=stability.files, processors=8) screen.seqs(fasta=current, maxambig=0, maxlength=275) unique.seqs() count.seqs(name=current, group=current) align.seqs(fasta=current, reference=silva.v4.fasta) screen.seqs(fasta=current, count=current, start=1968, end=11550, maxhomop=8) filter.seqs(fasta=current, vertical=T, trump=.) pre.cluster(fasta=current, count=current, diffs=2) unique.seqs(fasta=current, count=current) pre.cluster(fasta=current, count=current, diffs=2) chimera.uchime(fasta=current, count=current, dereplicate=t) remove.seqs(fasta=current, accnos=current) classify.seqs(fasta=current, count=current, reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax, cutoff=80) remove.lineage(fasta=current, count=current, taxonomy=current, taxon=Chloroplast-Mitochondria-unknown-Archaea-Eukaryota) remove.groups(count=current, fasta=current, taxonomy=current, groups=Mock) cluster.split(fasta=current, count=current, taxonomy=current, splitmethod=classify, taxlevel=4, cutoff=0.15) make.shared(list=current, count=current, label=0.03) classify.otu(list=current, count=current, taxonomy=current, label=0.03) phylotype(taxonomy=current) make.shared(list=current, count=current, label=1) classify.otu(list=current, count=current, taxonomy=current, label=1)