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Table 3 MiniScrub reduces downstream assembly errors

From: De novo Nanopore read quality improvement using deep learning

  MECAT Raw MiniScrub + MECAT Canu Raw MiniScrub + Canu
% genome assembled 79.39% 99.86% 99.69% 99.71%
NGA50 242478 1053459 1055037 696460
LGA50 12 3 2 5
# of contigs 38 11 7 19
# mis-assembled contigs 28 5 2 2
# local mis-assemblies 209 4 5 3
# indels > 5 bp 1099 394 84 46
Runtime (hours) 2.5 9 80 9
  1. MiniScrub significantly improves assembly, tested with MECAT [32], increasing genome coverage and NGA50 while limiting LGA50, mis-assemblies, mismatches, and indels. Canu’s assembly had slightly reduced errors and misassemblies when reads were preprocessed with MiniScrub, but the assembly was more fractured, likely due in part to resolving large misassemblies and indels. Notably, Canu assembly of raw reads took about 3.5 days, while the MiniScrub+Canu pipeline took about 9 hours, likely due to a reduction in the amount of error correction needed in the latter situation. Results were evaluated using QUAST [33] Best performance numbers are shown in bold