initial commit, first part completed

16S_workflow.sh

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+#!/bin/bash
+raw_reads_dir=$1
+output_dir=$2
+
+#mkdir $output_dir
+#mkdir trimmed_reads
+#TRIM READS WITH ALIENTRIMMER
+#for R1 in $(ls $raw_reads_dir/*R1.fastq);
+#    do
+#        R2=`echo $R1 | sed 's/R1/R2/g'`
+#        oR1=`echo $R1 | sed 's/\.fastq/\.at\.fq/g'`
+#        oR1=`echo $oR1 | sed 's/fastq\///g'`
+#        oR2=`echo $R2 | sed 's/\.fastq/\.at\.fq/g'`
+#        oR2=`echo $oR2 | sed 's/fastq\///g'`
+#        java -jar soft/AlienTrimmer.jar -if $R1 -ir $R2 -q 20 -c databases/contaminants.fasta -of trimmed_reads/$oR1 -or trimmed_reads/$oR2
+#    done
+
+
+# MERGE READS AND OUTPUT FASTA
+mkdir fasta
+for R1 in $(ls trimmed_reads/*R1.at.fq);
+    do
+        R2=`echo $R1 | sed 's/R1/R2/g'`
+        outname=`echo $R1 | sed 's/_R1\.at\.fq/\.fasta/g'`
+        label=`echo $outname | sed 's/trimmed_reads\///g'`
+        outname=`echo $outname | sed 's/trimmed_reads/fasta/g'`
+        label=`echo $label | sed 's/\.fasta//g'`
+        soft/vsearch --fastq_mergepairs $R1 --reverse $R2 --fastaout $outname --label_suffix ";sample=$label;"
+    done
+
+# MERGE ALL FASTAS TO 'amplicon.fasta'
+cat fasta/*.fasta > fasta/amplicon.fasta
+
+