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

merge_lanes.sh

#! /bin/bash

# Taken from https://github.com/stephenturner/mergelanes/issues/1
# Exercise caution, does not work accurately in every case:
# Not working accurately for sample IDs like "A11_Barcodexxx_S11_L001_R1_001". 
# It cat together all L001 pertaining to sample ID A11 with different barcodes also

ls *R1* | cut -d _ -f 1 | sort | uniq \
    | while read id; do \
        cat $id*R1*.fastq.gz > $id.R1.fastq.gz;
        cat $id*R2*.fastq.gz > $id.R2.fastq.gz;
      done