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This is a file required by mothur to remove the primer and diversity region from the library construct. Mothur looks for the exact sequence, and only keeps sequences when the primer sequence is found. As a note, if you are using Phusion or another proof-reading polymerase, mismatches in the primer site within 4 bases from the 3' end are reverted to the template sequence (actually, NEB says that it will change anything within 10 bps of the 3' end), which would then be consequently discarded at the trim.seqs step. I typically change the last 4 from the 3' end of the primer to N's to be safe. Filtering sequences that don't match the primer sequence has been shown to improve the quality of the data (|\Zhou_2011.pdf).
#where the programs are called from
BIN=/data/spacocha/bin
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