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Table 3 The running time (hour) and memory usage (Gb) for Pysim-sv simulations with different parameter settings

From: Pysim-sv: a package for simulating structural variation data with GC-biases

Simulation set up

Time

Memory

Genome Simulationa

One subclone with 100 SVs

0.98 h

9.1 Gb

 

One subclone with 200 SVs

1.34 h

9.9 Gb

 

One subclone with 300 SVs

1.73 h

11.6 Gb

 

Two subclones with 100 SVs

1.03 h

9.5 Gb

 

Three subclones with 100 SVs

1.28 h

10.2 Gb

Read generationb

Mixing reads from 2 subclones and 1 normal genome (392 M reads)

2.76 h

6.2 Gb

 

GC-bias Introduction (130 M reads)

4.10 h

2.5 GB

  1. aTime and memory usage for simulating subclone genomes and a normal genome
  2. bTime and memory usage for read generation by ART are not shown