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timbitz / Whippet.jl

Lightweight and Fast; RNA-seq quantification at the event-level
MIT License
105 stars 21 forks source link

Faster Whippet v0.5 #35

Closed timbitz closed 7 years ago

timbitz commented 7 years ago

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?

timbitz commented 7 years ago

This will close #34 as well.

timbitz commented 7 years ago

Current coverage is 44.90% (diff: 39.36%)

No coverage report found for master at b3623ef.

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