You can upload one or two (forward and reverse) fastq files. When you upload your data, the run will be be assigned a unique ID. Please take a note of this ID as you will need to to find your results later.
You can upload multiple samples together to batch process them. At the moment batch uploading only supports paried end reads. By default, files must use _1.fastq.gz and _2.fastq.gz as the file suffix in order for them to be paired correctly. The suffix can be changed in the advanced options.