BACTERIAL MICROBIOME ANALYSIS mothur > set.current(processors=12, fasta=180802_pratima.files.trim.contigs.fasta, group=180802_pratima.files.contigs.groups) mothur > summary.seqs(fasta=current) mothur > screen.seqs(fasta=current, group=current, maxambig=0, maxlength=375, minlength=367, maxhomop=8) mothur > summary.seqs() mothur > unique.seqs(fasta=current) mothur > count.seqs(name=current, group=current) mothur > summary.seqs(fasta=current, count=current) mothur > align.seqs(fasta=ecoli_align_silva.fas, reference=silva.gold.align) mothur > summary.seqs(fasta=ecoli_align_silva.align) mothur > get.current() mothur > pcr.seqs(fasta=silva.gold.align, start=13862, end=27654, keepdots=F) mothur > align.seqs(fasta=ecoli_align_silva.fas, reference=silva.nr_v132.align) mothur > summary.seqs(fasta=ecoli_align_silva.align) mothur > pcr.seqs(fasta=silva.nr_v132.align, start=13862, end=27654, keepdots=F) mothur > get.current() mothur > align.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.fasta, reference=silva.nr_v132.pcr.align) mothur > screen.seqs(fasta=current, count=current, start=13862, end=27654) mothur > unique.seqs(fasta=current, count=current) mothur > pre.cluster(fasta=current, count=current, diffs=3) mothur > chimera.vsearch(fasta=current, count=current, dereplicate=t) mothur > remove.seqs(fasta=current, accnos=current) mothur > summary.seqs(fasta=current, count=current) mothur > classify.seqs(fasta=current, count=current, reference=silva.nr_v132.align, taxonomy=silva.nr_v132.tax) mothur > remove.lineage(fasta=current, count=current, taxonomy=current, taxon=Chloroplast-Mitochondria-unknown-Archaea-Eukaryota) mothur > summary.tax(taxonomy=current, count=current) mothur > cluster.split(fasta=current, count=current, taxonomy=current, splitmethod=classify, taxlevel=4, cutoff=0.03) mothur > set.current(processors=12, fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, count=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table, taxonomy=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.nr_v132.wang.pick.taxonomy) mothur > cluster.split(fasta=current, count=current, taxonomy=current, splitmethod=classify, taxlevel=4, cutoff=0.03, method=opti) mothur > remove.rare(list=current, count=current, nseqs=10, label=0.03) mothur > make.shared(list=current, count=current, label=0.03) mothur > classify.otu(list=current, count=current, taxonomy=current, label=0.03) mothur > count.groups(shared=current) mothur > sub.sample(shared=current, size=6496) mothur > quit