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Simulate Genomes

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

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.

Usage

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

Output

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