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performance-comparison.md

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Performance comparison with other tools

Simulome

We tested the performance of Mutation-Simulator version 2 against Simulome, simulating SNPs, insertions and deletions with a rate of 0.000825 per base each on an E.coli str. K-12 genome. In this test Mutation-Simulator performed 24 times faster than Simulome.

Program Parameters Runtime [s] Memory peak [MB]
Mutation-Simulator ecoli_genome.fasta args -sn 0.000825353 -in 0.000825353 -de 0.000825353 1.7 106.34
Simulome --genome=ecoli_genome.fasta --anno=ecoli_anno.gtf --output=output --snp=TRUE --num_snp=1 --whole_genome=TRUE --verbose=1 --indel=3 --ins_len=2 --num_ins=1 --del_len=2 --num_del=1 40.1 71.68
  • Testing Platform: Solus
  • Processor: Intel(R) Core(TM) i5-8265U CPU @ 1.60GHz
  • Mutation-Simulator version: 2
  • Measuring tool: memory-profiler

SVsim

We also tested its performance in deletions against SVsim on the same E.coli genome with a rate of 0.000098 deletions per base and it came out 207 times faster.

Program Parameters Runtime [s] Memory Peak [MB]
Mutation-Simulator ecoli_genome.fasta args -de 0.000098241 -del 2 1.1 105.98
SVsim -r ecoli_genome.fasta -o o/svsimfiles -i event 228.0 22.34
  • Testing Platform: Solus
  • Processor: Intel(R) Core(TM) i5-8265U CPU @ 1.60GHz
  • Mutation-Simulator version: 2
  • Measuring tool: memory-profiler

simuG

We also compared the performance of Mutation-Simulator version 2 against simuG simulating SNPs and InDels at a rate of 0.01 and 0.1 on a 10 Mb test sequence and Mutation-Simulator was 6785 times faster.

Program Parameters Runtime [s]
Mutation-Simulator 10Mb.fa args -sn 0.01 -in 0.005 -de 0.005 7
simuG -refseq 10Mb.fa -snp_count 100000 -indel_count 100000 -prefix output_prefix 47497
Mutation-Simulator 10Mb.fa args -sn 0.1 -in 0.05 -de 0.05 47
simuG -refseq 10Mb.fa -snp_count 1000000 -indel_count 1000000 -prefix output_prefix aborted after several days
  • Testing Platform: Solus
  • Processor: Intel(R) Core(TM) i5-8265U CPU @ 1.60GHz
  • Mutation-Simulator version: 2
  • Measuring tool: GNU time