It might be possible to shoehorn Ray into doing something like the 'Inchworm' part of Trinity:
I've had a bit of a hiatus from work on Ray due to additional projects, but I'm interested in seeing if this will work because the current transcriptome assembly programs have really high memory requirements. The memory requirements are odd because the transcript graphs should be simpler (fewer repeats because you're making things like proteins, so branches should be mostly due to different isoforms), and the transcriptome size is smaller than the genome size.
My guess is trying something like disabling the genome coverage graph functions -- with RNASeq the mean coverage is per-transcript, but there can be within-transcript bias -- and writing out sequences that have some minimum coverage level based on the average coverage for each disconnected graph.
I've had a bit of a hiatus from work on Ray due to additional projects, but I'm interested in seeing if this will work because the current transcriptome assembly programs have really high memory requirements. The memory requirements are odd because the transcript graphs should be simpler (fewer repeats because you're making things like proteins, so branches should be mostly due to different isoforms), and the transcriptome size is smaller than the genome size.
My guess is trying something like disabling the genome coverage graph functions -- with RNASeq the mean coverage is per-transcript, but there can be within-transcript bias -- and writing out sequences that have some minimum coverage level based on the average coverage for each disconnected graph.
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