#fastq_mergepairs command  
usearch -fastq_mergepairs SampleA_R1.fq -reverse SampleA_R2.fq -fastqout SampleA.merged.fq -relabel @ -fastq_maxdiffpct 10
usearch -fastq_mergepairs SampleB_R1.fq -reverse SampleB_R2.fq -fastqout SampleB.merged.fq -relabel @ -fastq_maxdiffpct 10
usearch -fastq_mergepairs SampleC_R1.fq -reverse SampleC_R2.fq -fastqout SampleC.merged.fq -relabel @ -fastq_maxdiffpct 10
#...

cat *.merged.fq > reads.merged.fq

#fastx_truncate command
usearch -fastx_truncate  reads.merged.fq  -fastqout  reads.truncate.fq -stripleft 17 -stripright 21

#fastq_filter command
usearch -fastq_filter  reads.truncate.fq  -fastqout  reads.filter.fq -fastq_eeout -fastq_maxee 1 -fastq_minlen 380 -fastq_maxns 6

#fastx_uniques command
usearch -fastx_uniques  reads.filter.fq  -fastqout  reads.uniques.fq  -sizeout -relabel Uniq  -strand both -uc all.uniques.uc -log all.uniques.log  -minuniquesize 2

#cluster_otus command
usearch -cluster_otus  reads.uniques.fq  -otus  reads.otus.fa  -uparseout out.up  -relabel OTU  -minsize 2  -id 0.97

#usearch_global command
usearch -usearch_global  reads.merged.fq  -db reads.otus.fa  -strand  both  -id 0.95 -otutabout  otu_table.txt  -maxaccepts 8 -maxrejects 256

#sintax command
uearch  -sintax  reads.otus.fa  -db  rdp_16s_v16s_sp.fa  -strand  both  -tabbedout  tax.txt  -sintax_cutoff  0.8  -maxaccepts 8 -maxrejects 256

awk -F'\t' 'ARGIND==1{ tax[$1]=$4; }ARGIND==2{ if(FNR==1){ print $0"\ttaxonomy"; }else{ if(tax[$1]){print $0"\t"tax[$1];}else{print $0"\tunknown"} } }'  tax.txt  otu_table.txt > otu_table_tax.txt

less otu_table_tax.txt|sed 's/*/unknown/g'|sed 's/,/;/g'> otu_table_tax.tmp

biom convert -i otu_table_tax.tmp  -o otu_table_tax.biom --table-type "OTU table" --to-json --process-obs-metadata taxonomy

#qiime command

qiime

filter_taxa_from_otu_table.py -i otu_table_tax.biom  -o  otu_table_tax_filter.biom -n p:Cyanobacteria/Chloroplast,unknown

single_rarefaction.py -i otu_table_tax_filter.biom -o otu_table_29718.biom -d 29718

biom convert -i otu_table_29718.biom  -o otu_table_29718.txt --to-tsv --header-key taxonomy