Merge MiSeq diagnostic images for easy eyeballing

miseq-qc.sh

#!/bin/bash
# usage: $0 <MiSeq output dir> <output dir>

dir=$1/Thumbnail_Images/L001
output=$2
number_of_tiles=$(grep FlowcellLayout ${1}/RunInfo.xml | cut -d = -f 5 | sed -e 's/[^0-9]*//g')

if [[ ! -d ${output} ]]; then
        mkdir ${output}
fi

for i in $(seq 1 $(ls -1 ${dir} | cut -c 2- | cut -d . -f 1 | sort -n | tail -n 1)); do
        for base in a c g t; do
                montage ${dir}/C${i}.1/*_${base}.jpg -tile ${number_of_tiles}x3 -geometry +0+0 ${dir}/tmp_${i}_${base}.jpg
        done
        montage ${dir}/tmp_${i}_?.jpg -tile 1x4 -geometry +0+0 -quality 25 ${output}/C$(printf '%03d' ${i}).jpg
        rm ${dir}/tmp_${i}_?.jpg
done