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Use minimizers of each molecule rather than the barcode to map sequences#131

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jwcodee merged 13 commits intomasterfrom
correct-Mapping
Jan 15, 2020
Merged

Use minimizers of each molecule rather than the barcode to map sequences#131
jwcodee merged 13 commits intomasterfrom
correct-Mapping

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@jwcodee jwcodee commented Dec 18, 2019

Fly

Assembly NG50 NGA50 # misassemblies Genome fraction (%)
Original 20,504,419 839,829 467 89.025
Edge intersection 18,548,285 720,198 329 77.852
Split minimizer based on graph 20,495,800 890,313 450 89.017
Split minimizer based on graph + orient with more pieces 20,495,800 968,954 473 88.988

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@lcoombe lcoombe left a comment

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Thanks for all this work, Johnathan!

Comment thread physlr/physlr.py Outdated
Comment thread physlr/physlr.py Outdated
@jwcodee jwcodee force-pushed the correct-Mapping branch 2 times, most recently from 0e6f2e5 to 488cd5a Compare December 20, 2019 23:35
Comment thread physlr/physlr.py Outdated
@jwcodee jwcodee force-pushed the correct-Mapping branch 2 times, most recently from 6c50523 to 9ebef40 Compare January 6, 2020 19:10
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Great work Johnathan!

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jwcodee commented Jan 7, 2020

Human

Assembly NG50 NGA50 # misassemblies Genome fraction (%)
Original 58,105,812 10,216,403 524 86.840
Split minimizer based on graph + orient with more pieces 58,105,812 11,827,259 642 86.846
Original + arcs 58,505,102 15,922,618 424 86.840
Split minimizer based on graph + orient with more pieces + arcs 58,505,102 16,023,878 610 86.846

I need to try turning off more orient more pieces

@jwcodee jwcodee merged commit dffbecd into master Jan 15, 2020
@jwcodee jwcodee deleted the correct-Mapping branch January 15, 2020 23:31
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2 participants