Supplementary Information:
Specifics of mother parameters for OTU classification of microbiome from CF and non-CF
sputum samples.
#pcr.seqs(fasta=silva.bacteria.fasta, start=11894, end=25319, keepdots=F) #system(mv
silva.bacteria.pcr.fasta silva.v4.fasta) #../mothur_analysis/silva.bacteria/silva.bacteria.pcr.fasta (path to tax
reference on Roseophage, KW) #change the name of the file from stability.files to whatever suits your
study make.con:gs(file=stability.files) screen.seqs(fasta=stability.trim.con:gs.fasta,
group=stability.con:gs.groups, maxambig=0, maxlength=270) unique.seqs() count.seqs(name=current,
group=current) align.seqs(fasta=current,
reference=../mothur_analysis/silva.bacteria/silva.bacteria.pcr.fasta) screen.seqs(fasta=current,
count=current, start=13862, end=23444, maxhomop=8) filter.seqs(fasta=current, ver:cal=T, trump=.)
pre.cluster(fasta=current, count=current, diffs=3) unique.seqs(fasta=current, count=current)
pre.cluster(fasta=current, count=current, diffs=3) chimera.uchime(fasta=current, count=current,
dereplicate=t) remove.seqs(fasta=current, accnos=current)
classify.seqs(fasta=stability.trim.con:gs.good.unique.good.filter.precluster.unique.precluster.pick.pick.fasta,
count=stability.trim.con:gs.good.unique.good.filter.preclu
ster.unique.precluster.uchime.pick.pick.count_table,
reference=../mothur_analysis/silva.bacteria/silva.bacteria.pcr.fasta,
taxonomy=../mothur_analysis/silva.bacteria/silva. bacteria.rdp.pcr.tax, cutoff=80)
remove.lineage(fasta=current, count=current, taxonomy=current, taxon=Chloroplast-Mitochondriaunknown-Archaea-Eukaryota) #remove.groups(count=current, fasta=current, taxonomy=current,
groups=Mock) cluster.split(fasta=current, count=current, taxonomy=current, splitmethod=classify,
taxlevel=6, cutoff=0.2) 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)