## Utilities / Merge FASTQ

### Description

Merge two or more FASTQ files together.

### Parameters

- Order by file name (yes, no) [yes]
- Compress merged file with gzip (yes, no) [yes]

### Details

Merges two or more FASTQ. Files can be uncompressed, compressed or mixture of the two.

There is an option to merge the files in alphabetical order by file name. This can be useful when e.g. merging set of paired end reads, where maintaining the order of reads within files is important.

Default option is to compress the merged file with gzip. This should be used in most cases as the files can be large.

### Output

The analysis output consists of the following depending on chosen parameters:

- merged.fq: Merged FASTQ files
- merged.fq.gz: Merged and compressed FASTQ files

### References

None