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A proof of concept for calling de novo transcripts #18
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- Added steps to call de novo transcripts.
- Added polishing threads.
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This pull request implements a simple proof-of-concept calling of de novo transcripts from the per-gene clusters generated by isONclust2. It works by constructing a spoa consensus (coding sequence) from a subsample of reads then iteratively polishing it with racon.
Then the full set of reads are mapped to the coding sequence and the transcript are called using stringtie and gffread.