2_backbone_541.sh: add analysis of backbone_541

src/2_backbone_541.sh

+# compute backbone length
+
+docker run -ti --volume "$(pwd)"/results:/root/results/ --volume "$(pwd)"/data:/root/data/ bioawk:1.0
+bioawk -c fastx '{ print $name", "length($seq) }' \
+  /root/data/fasta/final_assembly.fasta > /root/results/backbone_size.csv
+exit
+
+# get Backbone_541
+docker run -ti --volume "$(pwd)"/results:/root/results/ --volume "$(pwd)"/data:/root/data/ bioawk:1.0
+bioawk -c fastx '{ if($name = "Backbone_541") { print ">"$name; print $seq }}' \
+  /root/data/fasta/final_assembly.fasta > /root/results/backbone_541.fasta
+exit
+
+# map read on Backbone_541
+docker run -ti --volume "$(pwd)"/results:/root/results/ --volume "$(pwd)"/data:/root/data/ bowtie2:2.3.4.1
+bowtie2-build --threads 8 /root/results/backbone_541.fasta /root/results/backbone_541.index
+
+bowtie2 --very-sensitive -p 8 -x /root/results/backbone_541.index \
+--rg-id MR_550 \
+--rg PL:Illumina \
+--rg SM:MR_550 \
+-1 /root/results/fastq/trimming/MR_550_clean_trim_R1.fastq.gz \
+-2 /root/results/fastq/trimming/MR_550_clean_trim_R2.fastq.gz | \
+samblaster --addMateTags -M -i /dev/stdin | \
+sambamba view -t 8 --valid -S -f bam -l 0 /dev/stdin \
+-o /root/results/backbone_541_MR_550.bam
+
+bowtie2 --very-sensitive -p 8 -x /root/results/backbone_541.index \
+--rg-id MR_350 \
+--rg PL:Illumina \
+--rg SM:MR_350 \
+-1 /root/results/fastq/trimming/MR_350_clean_trim_R1.fastq.gz \
+-2 /root/results/fastq/trimming/MR_350_clean_trim_R2.fastq.gz | \
+samblaster --addMateTags -M -i /dev/stdin | \
+sambamba view -t 8 --valid -S -f bam -l 0 /dev/stdin \
+-o /root/results/backbone_541_MR_350.bam
+
+bowtie2 --very-sensitive -p 8 -x /root/results/backbone_541.index \
+--rg-id MR_350 \
+--rg PL:Illumina \
+--rg SM:MR_350 \
+-1 /root/results/fastq/trimming/NG-10944_JU2859_bis_lib169352_5217_1_trim_R1.fastq.gz \
+-2 /root/results/fastq/trimming/NG-10944_JU2859_bis_lib169352_5217_1_trim_R2.fastq.gz | \
+samblaster --addMateTags -M -i /dev/stdin | \
+sambamba view -t 8 --valid -S -f bam -l 0 /dev/stdin \
+-o /root/results/backbone_541_JU2859.bam
+exit
+
+ ~/scripts/sms.sh "mapping done !"