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time split_libraries.py -m map.txt -q all560.fasta.qual -f all5.fa -b 10 -z truncate_only --reverse_primer_mismatches 1 -o PS560
time pick_de_novo_otus.py -i PS560/seqs.fna -o PS560/OTUs
time make_otu_network.py -m map.txt -i PS560/OTUs/otu_table.biom -o PS560/NETWORK
time make_otu_heatmap.py -i PS560/OTUs/otu_table.biom -o PS560/HEATMAP
time make_otu_heatmap_html.py -m map.txt -i PS560/OTUs/otu_table.biom -o PS560/HEATMAP
time summarize_taxa_through_plots.py -i PS560/OTUs/otu_table.biom -o PS560/SUMMARY -m map.txt -s
<>
echo "alpha_diversity:metrics shannon,PD_whole_tree,chao1,observed_species" > alpha
time alpha_rarefaction.py -i OTUs/otu_table.biom -m ../map.txt -o RAREF -p alpha -t OTUs/rep_set.tre
time beta_diversity_through_plots.py -i OTUs/otu_table.biom -m ../map.txt -o BETAR -t OTUs/rep_set.tre -e 200
time jackknifed_beta_diversity.py -m ../map.txt -i OTUs/otu_table.biom -t OTUs/rep_set.tre -o JACK -e 110
time make_emperor.py -i ./BETAR/unweighted_unifrac_pc.txt -m ../map.txt -t SUMMARY/otu_table_sorted_L3.txt --n_taxa_to_keep 5 -o BIPLOTS
time make_bootstrapped_tree.py -m JACK/unweighted_unifrac/upgma_cmp/master_tree.tre -s JACK/unweighted_unifrac/upgma_cmp/jackknife_support.txt -o JACK/jackknife_named_nodes.pdf
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