58 lines
2.0 KiB
Bash
Executable File
58 lines
2.0 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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# REMOVE ' ' FROM EACH READ NAME
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sed -i 's/ //g' fasta/amplicon.fasta
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# CREATE OTU
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# DEDUPLICATION
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mkdir otu
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soft/vsearch --derep_fulllength fasta/amplicon.fasta --output fasta/fulllength.fasta
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soft/vsearch --derep_prefix fasta/amplicon.fasta --output fasta/prefix.fasta
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# REMOVING SINGLETON
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soft/vsearch --derep_prefix fasta/amplicon.fasta --output fasta/prefix_min10.fasta --minuniquesize 10
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# REMOVING CHIMERAS
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soft/vsearch --uchime_denovo fasta/prefix.fasta --nonchimeras fasta/prefix_nochim.fasta
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# CLUSTERING
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otu=">OTU_"
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vsearch --cluster_fast fasta/prefix_nochim.fasta --id 0.97 --centroids otu/otu.fasta --relabel $otu
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# ABONDANCE
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vsearch --usearch_global fasta/amplicon.fasta --db otu/otu.fasta --id 0.97 --otutabout otu/abondance_table.txt
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# ANNOTATION
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soft/vsearch --usearch_global otu/otu.fasta --db databases/mock_16S_18S.fasta --id 0.97 --top_hits_only --userfields query+target --userout otu/annotation.txt
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