SeqFS: RNA Fold Change

SeqFS is a project intended to simplify processing and analysis of RNA [and hopyfully later DNA] sequences for biologists generating this kind of data in the lab.
The aim is to feed in raw fastq/fasta files to the program, and get files as output viewable on any genome browser, allowing researchers to compare fold change results for themselves.
Ideally this program will be run on a dedicated server with hefty compute resources, mainly for the sequence alignment step. However, the goal is to make it usable on any system, given enough time.