Seperate downstream analysis from datageneration for simulate_x_gb - Githubissues

HenrikSpiegel / Screener

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Seperate downstream analysis from datageneration for simulate_x_gb #3

Closed HenrikSpiegel closed 2 years ago

HenrikSpiegel commented 2 years ago

We need better seperation between data generation and data analysis.

Currently simulate_x_gb contains both the datageneration as well as analysis.

This should be split into:

[x] simulate_x_gb:
- Load genomes
- antismash genomes
- Run camisim.
[x] Quantification_by_mapping:
- Quality control
- Mapping
- quantification
- plotting/summary
[x] Quantification_by_kmer:
- Kmer abundances
- ...
[x] generate_kmer_catalogou:
- Determine distinct kmers
- Refine by agreement with negative binomial.

HenrikSpiegel commented 2 years ago

We have split into simulate and quantify for the simulated set.