https://bioinformaticsonline.com/snippets/view/37283/long-reads-mapper-bash-script? https://bioinformaticsonline.com/snippets/view/37283/long-reads-mapper-bash-script Thu, 12 Jul 2018 10:15:44 -0500 https://bioinformaticsonline.com/snippets/view/37283/long-reads-mapper-bash-script #!/bin/bash #only for LONG READS mapping #USAGE: runMapper.sh minimap2 ref.fa reads.fa/fq 48 ont echo -e "This is a bash scrip to map your long reads and make it visualization ready !" #Location of the tools samtools=/home/urbe/anaconda3/bin/samtools graphMapLoc=/home/urbe/Tools/graphmap/bin/Linux-x64/graphmap minimap2Loc=/home/urbe/Tools/minimap2-2.3_x64-linux/minimap2 bwaMemLoc=/home/urbe/anaconda3/bin/bwa ngmlrLoc=/home/urbe/Tools/ngmlr/bin/ngmlr-0.2.3/ngmlr lamsaLoc=/home/urbe/Tools/LAMSA/lamsa #Parameters accepted toolName=$1 refFasta=$2 longReads=$3 thread=$4 readsType=$5 if [ $# -lt 5 ]; then echo "No or less arguments provided" echo "#USAGE: runMapper.sh minimap2 ref.fa reads.fa/fq 48 ont" exit 1 fi fileName=$(basename "$refFasta"); #fileName=$(basename "$refFasta" .fq); echo "Name of the file used for mapping $fileName, present at $refFasta" if [ $toolName == "bwa" ]; then echo "Mapping with $toolName" $bwaMemLoc index $refFasta $bwaMemLoc mem $refFasta $longReads -t $thread > $fileName.out.sam elif [ $toolName == "lamsa" ]; then echo "Mapping with $toolName" $lamsaLoc index $refFasta if [ $readsType == "ont" ]; then $lamsaLoc aln -t $thread -T ont2d $refFasta $longReads > $fileName.out.sam elif [ $readsType == "pacbio" ]; then $lamsaLoc aln -t $thread -T pacbio $refFasta $longReads > $fileName.out.sam else echo "LAMSA:Please specify reads type: ont, pacbio" fi elif [ $toolName == "minimap2" ]; then echo "Mapping with $toolName" if [ $readsType == "ont" ]; then $minimap2Loc -ax map-ont $refFasta $longReads -t $thread > $fileName.out.sam elif [ $readsType == "pacbio" ]; then $minimap2Loc -ax map-pb $refFasta $longReads -t $thread > $fileName.out.sam else echo "MINIMAP2:Please specify reads type: ont, pacbio" fi elif [ $toolName == "ngmlr" ]; then echo "Mapping with $toolName" if [ $readsType == "ont" ]; then $ngmlrLoc -t $thread -r $refFasta -q $longReads -o $fileName.out.sam -x $readsType elif [ $readsType == "pacbio" ]; then $ngmlrLoc -t $thread -r $refFasta -q $longReads -o $fileName.out.sam -x $readsType else echo "NGMLR:Please specify reads type: ont, pacbio" fi elif [ $toolName == "graphmap" ]; then echo "Mapping with $toolName" $graphMapLoc align -r $refFasta -d $longReads -t $thread -o $fileName.out.sam else echo "Unknown mapper name and parameter !" fi echo "Getting files ready for visualization !" $samtools view -Sb $fileName.out.sam | $samtools sort -m 4G -@$thread -o $fileName.sorted.bam - && $samtools index -@$thread $fileName.sorted.bam echo "All Done :)"]]> Jit