Merge fastq files that belong to the same sample, but were generated from different lanes

merge_lanes.sh

#! /bin/bash

# Taken from https://www.biostars.org/p/317385/

#! /bin/bash

for i in $(find ./ -type f -name "*.fastq.gz" | while read F; do basename $F | rev | cut -c 22- | rev; done | sort | uniq)

    do echo "Merging R1"

echo "$i"_L00*_R1_001.fastq.gz
echo "$i"_ME_L001_R1_001.fastq

zcat "$i"_L00*_R1_001.fastq.gz > "$i"_ME_L001_R1_001.fastq

       echo "Merging R2"

zcat "$i"_L00*_R2_001.fastq.gz > "$i"_ME_L001_R2_001.fastq

echo "$i"_L00*_R2_001.fastq.gz
echo "$i"_ME_L001_R2_001.fastq

done;