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Table 8 Time and memory usage for overlap extension and assembly on viral metagenomic data from human plasam

From: TAR-VIR: a pipeline for TARgeted VIRal strain reconstruction from metagenomic data

   Time (m: minutes, h: hours) Memory (GB)
Mismatch rate 5% 10% 15% 20% 5% 10% 15% 20%
Overlap extension Building index 127m 127m 127m 127m 2.4 2.4 2.4 2.4
  Recruitment 8m 14m 20m 23m 3.5 3.5 3.5 3.5
De novo Assembly TAR-VIR 5m 7m 18m 20m 2 2.8 3.5 4
  SGA 2m 2m 3m 5m 0.9 0.9 0.9 0.9
  SPAdes 5m 5m 6m 8m 1 1 1 1
  SAVAGE 2h 8h 14h 18h 31 45 51 59
Reference-based assembly HaploClique    33h     5  
  Viquas    72h     4  
  drVM    23m     1  
Extension-based assembly PRICE    1h46m     5  
  1. The de novo assembly time and memory usage were evaluated on recruited reads based on mismatch rate from 5% to 20%. HaploClique, Viquas, drVM and PRICE were applied only on recruited reads based on mismatch rate of 15%
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