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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
-
- # REMOVE ' ' FROM EACH READ NAME
- sed -i 's/ //g' fasta/amplicon.fasta
-
- # CREATE OTU
- # DEDUPLICATION
- mkdir otu
- soft/vsearch --derep_fulllength fasta/amplicon.fasta --output fasta/fulllength.fasta
- soft/vsearch --derep_prefix fasta/amplicon.fasta --output fasta/prefix.fasta
-
- # REMOVING SINGLETON
- soft/vsearch --derep_prefix fasta/amplicon.fasta --output fasta/prefix_min10.fasta --minuniquesize 10
-
- # REMOVING CHIMERAS
- soft/vsearch --uchime_denovo fasta/prefix.fasta --nonchimeras fasta/prefix_nochim.fasta
-
- # CLUSTERING
- otu=">OTU_"
- vsearch --cluster_fast fasta/prefix_nochim.fasta --id 0.97 --centroids otu/centroids.fasta --relabel $otu
-
- # ABONDANCE
-
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