Illumina runs split each sample across lanes:

ID1_S99_L001_R1_001.fastq.gz
ID1_S99_L001_R2_001.fastq.gz
ID1_S99_L002_R1_001.fastq.gz
ID1_S99_L002_R2_001.fastq.gz
...

1. Merge

seqfu lanes groups the files by sample and strand and writes one file for each:

seqfu lanes -o merged/ raw/
ls merged/

ID1_R1.fastq  ID1_R2.fastq  ID2_R1.fastq  ID2_R2.fastq ...

The merged files are written uncompressed. The --extension option only changes the name
of the output files, so compress them afterwards (for example with gzip or pigz) rather
than passing -e .fastq.gz.

gzip merged/*.fastq

2. Check that no read was lost

The total number of reads per sample should match the sum over the lanes:

seqfu count raw/ID1_*_R1_*.fastq.gz
seqfu count merged/ID1_R1.fastq.gz