TABLE 4.

Bioinformatics pipeline for raw sequence data processing in mothur (version 1.39.5), showing commands, input file types and settings for each step

Command	Input files	Settings
unique.seqs	fasta
align.seqs	fasta, reference	reference=silva.nr_v128.V4
screen.seqs	fasta, group, name	start=1967, end=11549
filter.seqs	fasta	vertical=T, trump=.
pre.culster	fasta, group, name	diffs=2
chimera.uchime	fasta, group, name	dereplicate=t, reference=self
remove.seqs	fasta, group, name, accnos
classify.seqs	fasta, group, name	reference=gg_13_5_99.fasta, taxonomy=gg_13_5_99.pds.tax, cutoff=60
remove.lineage	fasta, group, name, taxonomy	taxon=Chloroplast-mitochondria-unknown-eukaryota
filter.seqs	fasta	vertical=T, trump=.
cluster	column, name	cutoff=0.03
remove.rare	list, group	nseqs=10, label=0.03
classify.otu	list, name, taxonomy	label=0.03
get.oturep	fasta, group, name, list	method=abundance, label=0.03
make.shared	list, group	label=0.03
sub.sample	list, group	size=22065, persample=t
list.otulabels	list
get.otulabels	accnoss, constaxonomy
make.shared	list, group