MergeLanes

mergelanes.sh

#Based on Stephen Turners and Wei Shen's ideas
# Works fine if your ID in the beginning is sort of (hehe) unique. 
# Comment out the cat part to run the dry run and check whether your output makes sense.
ls *R1* | cut -d _ -f 1 | sort | uniq \
    | while read id; do \
        echo "$id*R1*.fastq.gz >> $id.R1.fastq.gz";
        cat $id*R1*.fastq.gz >> $id.R1.fastq.gz;
        echo "$id*R2*.fastq.gz >> $id.R2.fastq.gz";
        cat $id*R2*.fastq.gz >> $id.R2.fastq.gz;
      done