Simulating transcriptome ONT reads

This is a pre-release version which is now capable of simulating both genomic and transcriptomic (cDNA and directRNA) ONT reads with even increased performance. Users may run the pipeline in "genome" or "transcriptome" mode. The transcriptome mode also models features of the library preparation protocols used, including intron retention events in cDNA and direct RNA reads. Further, it profiles transcript expression patterns.

We provided a very comprehensive README file for more information on how to run the pipeline in both modes.

Users who may have tried Trans-NanoSim before, can now rely on this version to simulate transcriptome ONT reads.

Major updates since pre-release v2.3-beta:

1. Added an optional flag (--uracil) to convert the thymine (T) bases to uracil (U) in the output fasta format. It is helpful if you are dealing with direct RNA reads.
2. Fixed a bug related to input file requirements when you use (--no_model_ir). Refer here: #63
3. Increased simulation speed substantially when IR modelling is not set (--no_model_ir). It performs 5-folds faster now. We also removed some redundant and unnecessary code lines to improve the overall performance of the pipeline.
4. As for "Perfect" reads (--perfect), we are now considering expression profiles when simulating them. Therefore your "perfect" error-free reads are going to follow your desired expression levels as well.

Please keep using the pipeline and share your thoughts on it. Cheers!