reference 'guided' consensus assembly

[ammaraziz]

From sola, process to generate a consensus from mapping + denovo.

#!/bin/bash

while IFS="," read -r sample_name      ref_strain      ref_file_name      R1_path      R2_path
do

bowtie2 -x  $ref_strain -1 $R1_path -2 $R2_path -S $sample_name"_"$ref_genome".sam" --local --threads 6

##convert sam to bam, sort, index, calculate genome coverage, convert bam to fastq
samtools view -bSh -o $sample_name".bam" $sample_name"_"$ref_genome".sam"
samtools sort $sample_name".bam" -o $sample_name"_sorted.bam"
samtools index $sample_name"_sorted.bam"
samtools coverage $sample_name"_sorted.bam" > $sample_name"_coverage.txt"

#bamToFastq 
bamToFastq -i $sample_name"_sorted.bam" -fq $sample_name"_refg_R1.fastq.gz" -fq2 $sample_name"_refg_R2.fastq.gz"

#Shovill final assembly:
shovill --outdir shovill/$sample_name"ref-guided" --gsize 1.04M --R1 $sample_name"_refg_R1.fastq.gz" --R2 $sample_name"_refg_R2.fastq.gz"

done < <(tail -n +1 purple_ref-genome_assembly_guide.csv)