Directory
mothur fig1
#! /Users/directoryname/mothur
system(cd /Users/directoryname)
#create master fasta file + corresponding group file
make.group(fasta=/Users/directoryname/filename_FV309R09_7.fasta-/Users/directoryname/filename_FV310R10_8.fasta-/Users/directoryname/filename_FV311R11_9.fasta-/Users/directoryname/filename_FV312R12_10.fasta-/Users/directoryname/filename_FV313R13_11.fasta-/Users/directoryname/filename_FV314R14_12.fasta-/Users/directoryname/filename_FV315R15_14.fasta-/Users/directoryname/filename_FV316R16_16.fasta, groups=7-8-9-10-11-12-14-16)
system(mv /Users/directoryname/filename_mergegroups /Users/directoryname/filename_mergedsamples.group)
merge.files(input=/Users/directoryname/filename_FV309R09_7.fasta-/Users/directoryname/filename_FV310R10_8.fasta-/Users/directoryname/filename_FV311R11_9.fasta-/Users/directoryname/filename_FV312R12_10.fasta-/Users/directoryname/filename_FV313R13_11.fasta-/Users/directoryname/filename_FV314R14_12.fasta-/Users/directoryname/filename_FV315R15_14.fasta-/Users/directoryname/filename_FV316R16_16.fasta, output=/Users/directoryname/filename_mergedsamples.fasta)
#sequence processing
summary.seqs(fasta=/Users/directoryname/filename_mergedsamples.fasta)
align.seqs(fasta=current, template=/Users/directoryname/Silva.nr_v123/silva.nr_v123.align, flip=T)
screen.seqs(fasta=current, group=/Users/directoryname/filename_mergedsamples.group, optimize=start-end, criteria=90)
filter.seqs(fasta=current, vertical=T, trump=.)
unique.seqs()
pre.cluster()
chimera.uchime(fasta=current, name=current)
remove.seqs(fasta=current, name=current, group=/Users/directoryname/filename_mergedsamples.group)
classify.seqs(fasta=current, name=current, group=current, template=/Users/directoryname/Silva.nr_v123/silva.nr_v123.align, taxonomy=/Users/directoryname/Silva.nr_v123/silva.nr_v123.tax, cutoff=80)