CUDA implementation of STAR aligner.
- This almost uses 75% code base from nvBowtie (GPU version of Bowtie2 aligner which is part of nvbio).
Changes from nvBowtie:
- Spliced alignments are the biggest challenege and the difference.
- Seeding (Maximum mapability length), in other words exact match of biggest substring of the read.
- Scoring is done by Sharon Entropy principle.