bioinformatics tool for RNA-seq data analysis: ideas wanted

[dovah]

Hi all

I'm planning to design a software tool for a bioinformatics programming project at university. It is mostly for fun during summer, but better if the software is useful and reusable for community, it would be more motivating. I have no restriction on software type, it can be anything. I mostly know python and bash, and not used to more low-level languages such as C++ or Java. A cute and useful script is what I am aiming at.

I have direct access to NGS RNA-seq data for D. melanogaster whole body females:
- Illumina HiSeq2500 paired-end reads (.fastq)
- Oxford MinION (.fast5, can be extracted to .fastq as well)

So, what would you suggest? Maybe, something related to isoform detection/benchamarking going besides the standard pipelines?

Thank you in advance for your ideas.

[gringer]

Use the illumina reads to generate ideal electrical sequence models, then try to match those models quickly to the MinION reads (event model, or raw signal).