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