Use grep --color=always to color a file by another file of patterns. Pretty useful for sequencing analysis

grep_color_barcodes.sh

color_grep_file() {
    COLOR_CMD="cat $1"
    echo $COLOR_CMD
    local i=31;
    while read line; do
        echo $line
        COLOR_CMD="$COLOR_CMD | GREP_COLOR='01;$i' grep --color=always -E '$line|$'"
        i=$(( $i + 1 ))
    done < $2
    COLOR_CMD="$COLOR_CMD | less -RS"
    bash -c "$COLOR_CMD"
}

Example:

color_grep_file <(paste fastq/S04926HPool10.1.fastq fastq/S04926HPool10.2.fastq | awk 'NR % 4 == 2') <(cut -f2 barcodes.txt)