This is a much faster version of Whippet which deprecates SGSequence in place of BioSequence and builds 2-bit indexes (not backwards compatible with Whippet v0.4). It has impressive speed benchmarks--> 25% faster than Whippet v0.4 for alignment, and 91% faster at building indexes!, and seems to align 1-2% more reads.
This version builds a fundamentally different index than all previous versions of Whippet because of its 2-bit encoding (there are no longer hard boundaries between adjacent nodes for seeding), and therefore needs accuracy and mapping benchmarks to proceed with merging this pull request. @weatheritt2 can you try this branch out for me?
This is a much faster version of Whippet which deprecates SGSequence in place of BioSequence and builds 2-bit indexes (not backwards compatible with Whippet v0.4). It has impressive speed benchmarks--> 25% faster than Whippet v0.4 for alignment, and 91% faster at building indexes!, and seems to align 1-2% more reads.
This version builds a fundamentally different index than all previous versions of Whippet because of its 2-bit encoding (there are no longer hard boundaries between adjacent nodes for seeding), and therefore needs accuracy and mapping benchmarks to proceed with merging this pull request. @weatheritt2 can you try this branch out for me?