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cd /project/microbiome/data_queue/seq/loc_ad1/otu

./run_slurm_mkotu.pl

Just analyzing trimmed R1s to avoid suspected merge/join bias because of 2 x 150 sequencing:

cd /project/microbiome/data/seq/TRNL_Test/tfmergedreads/16S/TRNL1/trimmed

cp ./*R1.fq /project/microbiome/data_queue/seq/TRNL_Test/

cd /project/microbiome/data/seq/TRNL_Test/

sed -n '1~4s/^@/>/p;2~4p' ./*.fq > ./TRNL_Test_16S.fa

vsearch -derep_fulllength --input TrnlTest16S.fa --output uniqueSequences.fa --sizeout --sizein

vsearch --derep_fulllength $s TrnlTest16S.fa \
        --strand plus \
        --output $s derep.fa \
        --sizeout \
        --uc $s.derep.uc \
        --relabel $s. \
        --fasta_width 0