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$job .= "cat $tfmdirectory/*tfmergedreads.fa $tfmdirectory/joined/*tfmergedreads.fa | vsearch --derep_fulllength - --threads 32 --output uniqueSequences.fa --sizeout;\n";
$job .= "vsearch --cluster_unoise uniqueSequences.fa --relabel 'otu' --sizein --sizeout --consout zotus.fa --minsize 8 ;\n";
$job .= "vsearch --uchime3_denovo zotus.fa --nonchimeras zotus_nonchimeric.fa --threads 32;\n";
$job .= "cat $tfmdirectory/*tfmergedreads.fa $tfmdirectory/joined/*tfmergedreads.fa | vsearch --usearch_global - --db zotus_nonchimeric.fa --otutabout - --id 0.99 --threads 32 | sed 's/^#OTU ID/OTUID/' > 'otutable';\n";
$job .= 'cat $tfmdirectory/*tfmergedreads.fa $tfmdirectory/joined/*tfmergedreads.fa | vsearch --search_exact ${WORKDIR}/tfmergedreads.fa- --db zotus_nonchimeric.fa --otutabout - --id 0.99 --threads 32'. " | sed 's/^#OTU ID/OTUID/' > 'otutable.esv';\n"; |
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