alignScript.sh

#!/bin/bash
# ./alignScript.sh ref pair1 pair2 name
ref_name=$1
pair1=$2
pair2=$3
name=$4
bwa index $ref_name
bwa mem $ref_name $pair1 $pair2 > ${name}.sam
samtools sort ${name}.sam -o ${name}.bam
samtools index ${name}.bam
rm ${name}.sam
samtools idxstats ${name}.bam
weeSAM --bam ${name}.bam --html ${name} --overwrite
samtools mpileup -aa -d 0 -Q 0 ${name}.bam | ivar consensus -p ${name}