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16S_workflow
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added merging, deduplication

master
nicolas-zimmermann 2019-10-23 17:25:39 +02:00
parent d57ea41f99
commit a84bce7c31
1 changed files with 22 additions and 11 deletions
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33
16S_workflow.sh
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@ -2,18 +2,18 @@
raw_reads_dir=$1
output_dir=$2
#mkdir $output_dir
#mkdir trimmed_reads
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
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
@ -31,4 +31,15 @@ for R1 in $(ls trimmed_reads/*R1.at.fq);
# 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 otu/fulllength_otu
soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_otu
# REMOVING SINGLETON
soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_min10_otu --minuniquesize 10
soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_min10_otu --minuniquesize 10