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trimmadapt.V1V2.sh
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trimmadapt.V1V2.sh
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#!/bin/bash
#
# copyright Pedro Martinez Arbizu & Sahar Khodami (2023)
#
### Trimm primers and adapters with bbmap
###use bbmap from https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
# run like: bash ./trimmadpat.sh > log.txt 2>&1 &
#####################################
### EDIT THESE OPTIONS ###
#####################################
# bbmap path
bbpath='/Dataexchange/bbmap'
# raw sequence path
RS="/Dataexchange/dada2batch/rawseq"
#Primer V1V2
primer='GCTTGTCTCAAAGATTAAGCC,GCCTGCTGCCTTCCTTGGA'
# kmer size for searching primer
# should be at most size of primer
k=15
# Hamming distance allowed
hd=1
#####################################
### Do NOT EDIT BEXOND THIS LINE ###
#####################################
for f in $RS/*_R1_*.fastq.gz; do
r=$(sed -e "s/_R1_/_R2_/" <<< "$f")
s=$(cut -d_ -f1 <<< "$f")
#for f in $RS/*_R1_*.fastq; do
#r=$(sed -e "s/_R1_/_R2_/" <<< "$f")
#s=$(cut -d_ -f1 <<< "$f")
echo ====================================
echo "Step 1 : Trimm adapter overhang using paired-end reads and primer sequence"
echo "processing $s"
echo ====================================
echo
$bbpath/bbduk.sh in1=$f in2=$r out1=$s\_R1_tr.fastq out2=$s\_R2_tr.fastq literal=$primer \
copyundefined ktrim=l k=$k hdist=$hd rcomp=t tbo overwrite=true
echo
echo
done
# move on with dada2
# nohup Rscript --vanilla SGN_dada2_batch.r &