Hi

If you need too see data in sequence or alignment view - the limit of UGENE is  about 1 Gb per file because the data is loaded to memory. Regardless of 32 or 64 bit system you have - the limitation is in a data model: we use 32 bit variables to store data sizes.

If you work with UGENE Assembly Browser  (BAM, SAM, FASTQ files) - it uses underlying database and can handle greater volumes (tested up to 100Gb) easily since the data is loaded by parts.

We plan to overcome this limit and make all views/algorithms in UGENE to work with large data volumes. Actually this is a main goal for 2.0 release. So sequence and alignment views that are used to show most of the data formats today will be rewritten till winter.