Mothur

 # Commands are from the tutorial in reference section

 # Make contigs
 mothur "#make.contigs(file=horse.files, processors=2)"

 # Summarize results
 mothur "#summary.seqs(fasta=SRR952153_1.trim.contigs.fasta, processors=2)" 

 # Remove outliers
 mothur "#screen.seqs(fasta=SRR952153_1.trim.contigs.fasta, group=SRR952153_1.contigs.groups, maxambig=0, minlength=250, maxlength=260)"

 # unique sequences
 mothur "#unique.seqs(fasta=horse.m.s.fasta)" 
 mothur "#count.seqs(name=horse.m.s.names, group=horse.m.s.groups)"