data preprocessing fig4

#! /bin/bash

## Sequencing data analysis pipeline


#Set up working directory
cd /Users/directoryname


###################
## FastX toolkit ##
###################

#Convert fastq file to fasta
fastq_to_fasta -i filename.fastq -o filename.fasta

#Reverse-complement all reads and add these "new" sequences to the original file
fastx_reverse_complement -i filename.fasta -o filename_revcompl.fasta
cat filename.fasta filename_revcompl.fasta > filename_ALL.fasta

#Convert fasta file to tab-delimited txt file and swap columns (sequences/names)
fasta_formatter -t -i filename_ALL.fasta -o filename_ALL_tab.txt
join -o 1.2,1.1 filename_ALL_tab.txt filename_ALL_tab.txt > filename_ALL_tab_swaped.txt


#Select reads matching FWD and REV primer (+barcode) sequences
grep -E "^CAAGGATGTCACTCCTACGGGAGGCAGCAGT" filename_ALL_tab_swaped.txt > filename_F09.txt
grep -E "^CTCAACAGTCACTCCTACGGGAGGCAGCAGT" filename_ALL_tab_swaped.txt > filename_F10.txt
grep -E "^CGTAGCTATCACTCCTACGGGAGGCAGCAGT" filename_ALL_tab_swaped.txt > filename_F11.txt
grep -E "^CATGAGCTTCACTCCTACGGGAGGCAGCAGT" filename_ALL_tab_swaped.txt > filename_F12.txt
grep -E "^CAGATCTGTCACTCCTACGGGAGGCAGCAGT" filename_ALL_tab_swaped.txt > filename_F13.txt
grep -E "^CCTACCATTCACTCCTACGGGAGGCAGCAGT" filename_ALL_tab_swaped.txt > filename_F14.txt
grep -E "^CCGCAATATCACTCCTACGGGAGGCAGCAGT" filename_ALL_tab_swaped.txt > filename_F15.txt
grep -E "^CTCACACTTCACTCCTACGGGAGGCAGCAGT" filename_ALL_tab_swaped.txt > filename_F16.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGCATCCTTG" filename_F09.txt > filename_F09R09_AB1.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGCTGTTGAG" filename_F09.txt > filename_F09R10_A1.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGTAGCTACG" filename_F09.txt > filename_F09R11_A2.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGAGCTCATG" filename_F09.txt > filename_F09R12_A3.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGCAGATCTG" filename_F09.txt > filename_F09R13_A10.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGATGGTAGG" filename_F09.txt > filename_F09R14_A11.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGTATTGCGG" filename_F09.txt > filename_F09R15_A12.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGAGTGTGAG" filename_F09.txt > filename_F09R16_A8.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGCTGTTGAG" filename_F10.txt > filename_F10R10_AB2.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGTAGCTACG" filename_F10.txt > filename_F10R11_TPCR.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGAGCTCATG" filename_F10.txt > filename_F10R12_TEXT.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGCAGATCTG" filename_F10.txt > filename_F10R13_TLAB.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGTATTGCGG" filename_F10.txt > filename_F10R15_A9.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGTAGCTACG" filename_F11.txt > filename_F11R11_AB3.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGATGGTAGG" filename_F11.txt > filename_F11R14_B4.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGAGCTCATG" filename_F12.txt > filename_F12R12_AB4.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGCAGATCTG" filename_F12.txt > filename_F12R13_B5.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGAGCTCATG" filename_F13.txt > filename_F13R12_B6.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGCAGATCTG" filename_F13.txt > filename_F13R13_A4.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGTAGCTACG" filename_F14.txt > filename_F14R11_B7.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGATGGTAGG" filename_F14.txt > filename_F14R14_A5.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGCTGTTGAG" filename_F15.txt > filename_F15R10_B8.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGTATTGCGG" filename_F15.txt > filename_F15R15_A6.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGCATCCTTG" filename_F16.txt > filename_F16R09_B9.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGCTGTTGAG" filename_F16.txt > filename_F16R10_B1.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGTAGCTACG" filename_F16.txt > filename_F16R11_B2.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGAGCTCATG" filename_F16.txt > filename_F16R12_B3.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGCAGATCTG" filename_F16.txt > filename_F16R13_B10.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGATGGTAGG" filename_F16.txt > filename_F16R14_B11.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGTATTGCGG" filename_F16.txt > filename_F16R15_B12.txt
grep -E "GTGTAG(C|A)GGTGAAAT(G|T)CGTGAGTGTGAG" filename_F16.txt > filename_F16R16_A7.txt

#Convert tabular file to fasta
awk '{print ">"$2"\n"$1}' filename_F09R09_AB1.txt > filename_F09R09_AB1.fasta
awk '{print ">"$2"\n"$1}' filename_F09R10_A1.txt > filename_F09R10_A1.fasta
awk '{print ">"$2"\n"$1}' filename_F09R11_A2.txt > filename_F09R11_A2.fasta
awk '{print ">"$2"\n"$1}' filename_F09R12_A3.txt > filename_F09R12_A3.fasta
awk '{print ">"$2"\n"$1}' filename_F09R13_A10.txt > filename_F09R13_A10.fasta
awk '{print ">"$2"\n"$1}' filename_F09R14_A11.txt > filename_F09R14_A11.fasta
awk '{print ">"$2"\n"$1}' filename_F09R15_A12.txt > filename_F09R15_A12.fasta
awk '{print ">"$2"\n"$1}' filename_F09R16_A8.txt > filename_F09R16_A8.fasta
awk '{print ">"$2"\n"$1}' filename_F10R10_AB2.txt > filename_F10R10_AB2.fasta
awk '{print ">"$2"\n"$1}' filename_F10R11_TPCR.txt > filename_F10R11_TPCR.fasta
awk '{print ">"$2"\n"$1}' filename_F10R12_TEXT.txt > filename_F10R12_TEXT.fasta
awk '{print ">"$2"\n"$1}' filename_F10R13_TLAB.txt > filename_F10R13_TLAB.fasta
awk '{print ">"$2"\n"$1}' filename_F10R15_A9.txt > filename_F10R15_A9.fasta
awk '{print ">"$2"\n"$1}' filename_F11R11_AB3.txt > filename_F11R11_AB3.fasta
awk '{print ">"$2"\n"$1}' filename_F11R14_B4.txt > filename_F11R14_B4.fasta
awk '{print ">"$2"\n"$1}' filename_F12R12_AB4.txt > filename_F12R12_AB4.fasta
awk '{print ">"$2"\n"$1}' filename_F12R13_B5.txt > filename_F12R13_B5.fasta
awk '{print ">"$2"\n"$1}' filename_F13R12_B6.txt > filename_F13R12_B6.fasta
awk '{print ">"$2"\n"$1}' filename_F13R13_A4.txt > filename_F13R13_A4.fasta
awk '{print ">"$2"\n"$1}' filename_F14R11_B7.txt > filename_F14R11_B7.fasta
awk '{print ">"$2"\n"$1}' filename_F14R14_A5.txt > filename_F14R14_A5.fasta
awk '{print ">"$2"\n"$1}' filename_F15R10_B8.txt > filename_F15R10_B8.fasta
awk '{print ">"$2"\n"$1}' filename_F15R15_A6.txt > filename_F15R15_A6.fasta
awk '{print ">"$2"\n"$1}' filename_F16R09_B9.txt > filename_F16R09_B9.fasta
awk '{print ">"$2"\n"$1}' filename_F16R10_B1.txt > filename_F16R10_B1.fasta
awk '{print ">"$2"\n"$1}' filename_F16R11_B2.txt > filename_F16R11_B2.fasta
awk '{print ">"$2"\n"$1}' filename_F16R12_B3.txt > filename_F16R12_B3.fasta
awk '{print ">"$2"\n"$1}' filename_F16R13_B10.txt > filename_F16R13_B10.fasta
awk '{print ">"$2"\n"$1}' filename_F16R14_B11.txt > filename_F16R14_B11.fasta
awk '{print ">"$2"\n"$1}' filename_F16R15_B12.txt > filename_F16R15_B12.fasta
awk '{print ">"$2"\n"$1}' filename_F16R16_A7.txt > filename_F16R16_A7.fasta


##############
## Cutadapt ##
##############

#remove 5'adapters
cutadapt -g CAAGGATGTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F09R09_AB1.fasta > filename_F09R09_AB1_.fasta 2> cutadapt-report_AB1_.txt
cutadapt -g CAAGGATGTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F09R10_A1.fasta > filename_F09R10_A1_.fasta 2> cutadapt-report_A1_.txt
cutadapt -g CAAGGATGTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F09R11_A2.fasta > filename_F09R11_A2_.fasta 2> cutadapt-report_A2_.txt
cutadapt -g CAAGGATGTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F09R12_A3.fasta > filename_F09R12_A3_.fasta 2> cutadapt-report_A3_.txt
cutadapt -g CAAGGATGTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F09R13_A10.fasta > filename_F09R13_A10_.fasta 2> cutadapt-report_A10_.txt
cutadapt -g CAAGGATGTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F09R14_A11.fasta > filename_F09R14_A11_.fasta 2> cutadapt-report_A11_.txt
cutadapt -g CAAGGATGTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F09R15_A12.fasta > filename_F09R15_A12_.fasta 2> cutadapt-report_A12_.txt
cutadapt -g CAAGGATGTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F09R16_A8.fasta > filename_F09R16_A8_.fasta 2> cutadapt-report_A8_.txt
cutadapt -g CTCAACAGTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F10R10_AB2.fasta > filename_F10R10_AB2_.fasta 2> cutadapt-report_AB2_.txt
cutadapt -g CTCAACAGTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F10R11_TPCR.fasta > filename_F10R11_TPCR_.fasta 2> cutadapt-report_TPCR_.txt
cutadapt -g CTCAACAGTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F10R12_TEXT.fasta > filename_F10R12_TEXT_.fasta 2> cutadapt-report_TEXT_.txt
cutadapt -g CTCAACAGTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F10R13_TLAB.fasta > filename_F10R13_TLAB_.fasta 2> cutadapt-report_TLAB_.txt
cutadapt -g CTCAACAGTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F10R15_A9.fasta > filename_F10R15_A9_.fasta 2> cutadapt-report_A9_.txt
cutadapt -g CGTAGCTATCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F11R11_AB3.fasta > filename_F11R11_AB3_.fasta 2> cutadapt-report_AB3_.txt
cutadapt -g CGTAGCTATCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F11R14_B4.fasta > filename_F11R14_B4_.fasta 2> cutadapt-report_B4_.txt
cutadapt -g CATGAGCTTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F12R12_AB4.fasta > filename_F12R12_AB4_.fasta 2> cutadapt-report_AB4_.txt
cutadapt -g CATGAGCTTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F12R13_B5.fasta > filename_F12R13_B5_.fasta 2> cutadapt-report_B5_.txt
cutadapt -g CAGATCTGTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F13R12_B6.fasta > filename_F13R12_B6_.fasta 2> cutadapt-report_B6_.txt
cutadapt -g CAGATCTGTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F13R13_A4.fasta > filename_F13R13_A4_.fasta 2> cutadapt-report_A4_.txt
cutadapt -g CCTACCATTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F14R11_B7.fasta > filename_F14R11_B7_.fasta 2> cutadapt-report_B7_.txt
cutadapt -g CCTACCATTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F14R14_A5.fasta > filename_F14R14_A5_.fasta 2> cutadapt-report_A5_.txt
cutadapt -g CCGCAATATCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F15R10_B8.fasta > filename_F15R10_B8_.fasta 2> cutadapt-report_B8_.txt
cutadapt -g CCGCAATATCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F15R15_A6.fasta > filename_F15R15_A6_.fasta 2> cutadapt-report_A6_.txt
cutadapt -g CTCACACTTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F16R09_B9.fasta > filename_F16R09_B9_.fasta 2> cutadapt-report_B9_.txt
cutadapt -g CTCACACTTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F16R10_B1.fasta > filename_F16R10_B1_.fasta 2> cutadapt-report_B1_.txt
cutadapt -g CTCACACTTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F16R11_B2.fasta > filename_F16R11_B2_.fasta 2> cutadapt-report_B2_.txt
cutadapt -g CTCACACTTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F16R12_B3.fasta > filename_F16R12_B3_.fasta 2> cutadapt-report_B3_.txt
cutadapt -g CTCACACTTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F16R13_B10.fasta > filename_F16R13_B10_.fasta 2> cutadapt-report_B10_.txt
cutadapt -g CTCACACTTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F16R14_B11.fasta > filename_F16R14_B11_.fasta 2> cutadapt-report_B11_.txt
cutadapt -g CTCACACTTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F16R15_B12.fasta > filename_F16R15_B12_.fasta 2> cutadapt-report_B12_.txt
cutadapt -g CTCACACTTCACTCCTACGGGAGGCAGCAGT -e 0.04 --minimum-length=200 filename_F16R16_A7.fasta > filename_F16R16_A7_.fasta 2> cutadapt-report_A7_.txt


#remove 3'adapters
cutadapt -a GTGTAGCAGGTGAAATGTCGTGCATCCTTG -e 0.08 --minimum-length=200 filename_F09R09_AB1_.fasta > filename_AB1.fasta 2> cutadapt-report_AB1.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGCTGTTGAG -e 0.08 --minimum-length=200 filename_F09R10_A1_.fasta > filename_A1.fasta 2> cutadapt-report_A1.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGTAGCTACG -e 0.08 --minimum-length=200 filename_F09R11_A2_.fasta > filename_A2.fasta 2> cutadapt-report_A2.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGAGCTCATG -e 0.08 --minimum-length=200 filename_F09R12_A3_.fasta > filename_A3.fasta 2> cutadapt-report_A3.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGCAGATCTG -e 0.08 --minimum-length=200 filename_F09R13_A10_.fasta > filename_A10.fasta 2> cutadapt-report_A10.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGATGGTAGG -e 0.08 --minimum-length=200 filename_F09R14_A11_.fasta > filename_A11.fasta 2> cutadapt-report_A11.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGTATTGCGG -e 0.08 --minimum-length=200 filename_F09R15_A12_.fasta > filename_A12.fasta 2> cutadapt-report_A12.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGAGTGTGAG -e 0.08 --minimum-length=200 filename_F09R16_A8_.fasta > filename_A8.fasta 2> cutadapt-report_A8.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGCTGTTGAG -e 0.08 --minimum-length=200 filename_F10R10_AB2_.fasta > filename_AB2.fasta 2> cutadapt-report_AB2.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGTAGCTACG -e 0.08 --minimum-length=200 filename_F10R11_TPCR_.fasta > filename_TPCR.fasta 2> cutadapt-report_TPCR.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGAGCTCATG -e 0.08 --minimum-length=200 filename_F10R12_TEXT_.fasta > filename_TEXT.fasta 2> cutadapt-report_TEXT.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGCAGATCTG -e 0.08 --minimum-length=200 filename_F10R13_TLAB_.fasta > filename_TLAB.fasta 2> cutadapt-report_TLAB.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGTATTGCGG -e 0.08 --minimum-length=200 filename_F10R15_A9_.fasta > filename_A9.fasta 2> cutadapt-report_A9.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGTAGCTACG -e 0.08 --minimum-length=200 filename_F11R11_AB3_.fasta > filename_AB3.fasta 2> cutadapt-report_AB3.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGATGGTAGG -e 0.08 --minimum-length=200 filename_F11R14_B4_.fasta > filename_B4.fasta 2> cutadapt-report_B4.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGAGCTCATG -e 0.08 --minimum-length=200 filename_F12R12_AB4_.fasta > filename_AB4.fasta 2> cutadapt-report_AB4.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGCAGATCTG -e 0.08 --minimum-length=200 filename_F12R13_B5_.fasta > filename_B5.fasta 2> cutadapt-report_B5.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGAGCTCATG -e 0.08 --minimum-length=200 filename_F13R12_B6_.fasta > filename_B6.fasta 2> cutadapt-report_B6.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGCAGATCTG -e 0.08 --minimum-length=200 filename_F13R13_A4_.fasta > filename_A4.fasta 2> cutadapt-report_A4.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGTAGCTACG -e 0.08 --minimum-length=200 filename_F14R11_B7_.fasta > filename_B7.fasta 2> cutadapt-report_B7.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGATGGTAGG -e 0.08 --minimum-length=200 filename_F14R14_A5_.fasta > filename_A5.fasta 2> cutadapt-report_A5.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGCTGTTGAG -e 0.08 --minimum-length=200 filename_F15R10_B8_.fasta > filename_B8.fasta 2> cutadapt-report_B8.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGTATTGCGG -e 0.08 --minimum-length=200 filename_F15R15_A6_.fasta > filename_A6.fasta 2> cutadapt-report_A6.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGCATCCTTG -e 0.08 --minimum-length=200 filename_F16R09_B9_.fasta > filename_B9.fasta 2> cutadapt-report_B9.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGCTGTTGAG -e 0.08 --minimum-length=200 filename_F16R10_B1_.fasta > filename_B1.fasta 2> cutadapt-report_B1.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGTAGCTACG -e 0.08 --minimum-length=200 filename_F16R11_B2_.fasta > filename_B2.fasta 2> cutadapt-report_B2.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGAGCTCATG -e 0.08 --minimum-length=200 filename_F16R12_B3_.fasta > filename_B3.fasta 2> cutadapt-report_B3.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGCAGATCTG -e 0.08 --minimum-length=200 filename_F16R13_B10_.fasta > filename_B10.fasta 2> cutadapt-report_B10.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGATGGTAGG -e 0.08 --minimum-length=200 filename_F16R14_B11_.fasta > filename_B11.fasta 2> cutadapt-report_B11.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGTATTGCGG -e 0.08 --minimum-length=200 filename_F16R15_B12_.fasta > filename_B12.fasta 2> cutadapt-report_B12.txt
cutadapt -a GTGTAGCAGGTGAAATGTCGTGAGTGTGAG -e 0.08 --minimum-length=200 filename_F16R16_A7_.fasta > filename_A7.fasta 2> cutadapt-report_A7.txt