This pipeline is designed to simulate full genomes, derived from reference genomes, with some genomic variation. The intention of this pipeline is to be used as a tool to create datasets that can be used as part of a validation experiment for other microbial genomics analysis pipelines.
Dependencies are listed in environments.yml. When using the conda profile, they will be installed automatically.
Other runtime environments such as docker, podman or singularity are not currently supported.
The pipeline takes a single reference genome as input, in FASTA format.
To run the pipeline with default parameters:
nextflow run dfornika/simulate-genomes \
-profile conda \
--cache ~/.conda/envs \
--ref </path/to/ref> \
--outdir </path/to/outdir>
Several parameters are available to control the amount of genomic variation that is introduced in the simulation process.
| Parameter | Description | Default |
|---|---|---|
min_snps |
Minimum number of SNPs that will be introduced. | 0 |
max_snps |
Maximum number of SNPs that will be introduced. | 1000 |
min_cnvs |
Minimum number of CNVs that will be introduced. | 0 |
max_cnvs |
Maximum number of CNVs that will be introduced. | 100 |
min_indels |
Minimum number of INDELs that will be introduced. | 0 |
max_indels |
Maximum number of INDELs that will be introduced. | 1000 |
For each simulated genome, a four-character semi-random string will be appended to the original input genome name. For example, starting with an input file named ATCC-BAA-2779.fasta
will generate the following outputs.
ATCC-BAA-2779-DCDE
├── ATCC-BAA-2779-DCDE.fa
├── ATCC-BAA-2779-DCDE_mutation_info.csv
├── ATCC-BAA-2779-DCDE_variants.tsv
└── ATCC-BAA-2779-DCDE.vcf