params

#locations
#main project directory
projdir=/mnt/nvme1n1p1/eDNA_Data
#name markers - for the MPA work, usually one or more of 12S, COI, 16S, 18S
marker1=12S
marker2=COI
markerN=16S

## Set up forward and reverse primer pairs for cutadapt
#COI Leray primers
LERAYXT=GGWACWRGWTGRACTITITAYCCYCC
LERAYF=GGWACWGGWTGAACWGTWTAYCCYCC
LERAYR=TAIACYTCIGGRTCICCRAARAAYCA

#MiFish forward and reverse and modified forward primers
MIFISHUF=GTCGGTAAAACTCGTGCCAGC
MIFISHUR=NNNNNNCATAGTGGGGTATCTAATCCCAGTTTG
MIFISHMOD=CGTGCCAGCCACCGCGGTT #this is the 248S_F primer developed by Royce Steeves

#16S Teleo
TeleoF=AGCGYAATCACTTGTCTYTTAA
TeleoR=CRBGGTCGCCCCAACCRAA

#18S primer sets - Comeau et al 2011 - E572F-E1009R
COMEF=CYGCGGTAATTCCAGCTC
COMER=AYGGTATCTRATCRTCTTYG

echo Primers for 12S, COI, 16S, and 18S are now loaded, please add any others you might need!