Genome synthesizer - Test error rate of ART-mbarc

[HenrikSpiegel]

Build a small genome "synthesizer" which generates genomes of varying GC content to test the influence of GC content on the error profile.

Goal of experiment.

What is the impact of varius GC content "genomes" on the error profile.

Approach:

• [ ] Build small script/notebook which can generate "genomes" with a given base distribution.
• [ ] Run map quantification
  • [ ] Run Camisim on the genome
  • [ ] Minimap2 to the genome
  • [ ] samtools stats -> extract per base error rate.
• [ ] Plot the per-base error rate as function of GC content.

[HenrikSpiegel]

10% GC content (reads from genomes ranging 0.1-0.9 GC content to the 0.1 GC genome): error rate: 3.064970e-02

50% GC content (reads from genomes ranging 0.1-0.9 GC content to the 0.5 GC genome): error rate: 3.061980e-02

10% GC content only simulating a single genome with 0.1 GC content: error rate: 3.060669e-02

Overall error on all genomes (0.1-0.9) all reads mapped to all genomes: error rate: 3.061503e-02