maybe a simpler way

[shenwei356]

cut is used to split id1_L001_R1_001.fastq.gz by _ to get the sample ID.

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

[stephenturner]

thanks added suggestion to README in 2c6e0f9 #2

[IshaMonga]

It's 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