#chimera.vsearch
# chimera.vsearch is a wrapper for the vsearch program written by https://github.com/torognes/vsearch
# chimera.fasta is stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta from MISeq_SOP
# chimera.count is stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table from MISeq_SOP
# name and group parameters untested, because the name and group files are auto converted to a count file before running
# this conversion is tested in the pre.cluster commands use of name and groups
# NOTE: download TestReferences and TestFiles and put in same location as mothur executable
set.dir(input=./TestFiles, output=./TestResults/chimera.vsearch, tempdefault=./TestReferences)
set.logfile(name=chimera.vsearch.logfile)
chimera.vsearch(fasta=chimera.fasta, reference=silva.gold.ng.fasta)
chimera.vsearch(fasta=chimera.fasta, count=chimera.count_table)
chimera.vsearch(fasta=chimera.fasta, count=chimera.count_table, dereplicate=t)
quit()
