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timbitz / Whippet.jl

Lightweight and Fast; RNA-seq quantification at the event-level
MIT License
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Streaming on-the-fly re-analysis of RNA-seq data from ebi.ac.uk #60

Closed timbitz closed 6 years ago

timbitz commented 6 years ago

--ebi and --url features are back by popular demand! @harpur @weatheritt2

In a less than scientific benchmark on my Macbook pro, the full re-analysis of a benchmark dataset SRR2300536 (22M paired-end reads) took ~37min with Whippet --ebi flag, meanwhile just downloading the dataset alone with wget took ~25mins.

codecov[bot] commented 6 years ago

Codecov Report

Merging #60 into 0.6-biasopt will increase coverage by 0.92%. The diff coverage is 62.85%.

Impacted file tree graph

@@               Coverage Diff               @@
##           0.6-biasopt      #60      +/-   ##
===============================================
+ Coverage        49.51%   50.43%   +0.92%     
===============================================
  Files               18       18              
  Lines             2361     2393      +32     
===============================================
+ Hits              1169     1207      +38     
+ Misses            1192     1186       -6
Impacted Files Coverage Δ
src/ebi.jl 80% <ø> (+80%) :arrow_up:
src/bias.jl 30.81% <0%> (-0.19%) :arrow_down:
src/reads.jl 30.18% <64.7%> (+17.03%) :arrow_up:
src/types.jl 87.5% <0%> (+50%) :arrow_up:

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