Performance comparison with other tools
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
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
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