Question: Should I use the Illumina Experiment Manager (IEM) or simple CSV format sample sheet for demultiplexing with mkfastq?
Answer: If you are using mkfastq we recommend using the simple CSV format in most situations due to its ease of use (only three columns), eliminating unnecessary fields and making it harder for syntax errors to hide. Here's an example:
Lane,Sample,Index 1,Sample1,SI-GA-A1 2,Sample2,SI-GA-A2
Some users may already be used to using the IEM format for demultiplexing, for example if they are already used to using bcl2fastq directly. In this case, the IEM is perfectly fine.
An important caveat is that if you did not sequence your index, you will need to use the IEM format.
When using the simple CSV format, you must use the --csv option to specify the path to your sample sheet. When using the IEM format, you must use the --samplesheet option.
For more information about bcl2fastq, please consult the Illumina documentation.