This repository contains the scripts used to simulate the reads for testing in the Katmon pipeline. The complete results of the simulated reads, semi-synthetic reads, and publicly available datasets can be found in the results directory.

To use the scripts for simulation:

• Determine lineages to simulate (eg. AY.132_and_AY.63)

• Edit proportions tsv file (assets/proportions.tsv) example:

  AY.132 50
  AY.63 50
  

• Run the pipeline to generate simulated reads (FASTQ) and create other Katmon input files (BAM and FASTA)

  nextflow run simKatmon \
  --sample <sample name including proportions> \
  --fasta <fasta file of lineages to simulate> \
  --out_dir <results dir>
  

example:

nextflow run simKatmon \
--sample AY.75_50_BA.2.5_50 \
--fasta /assets/lineages-ref-fasta/AY.132_and_AY.63.fasta \
--out_dir /simulated-reads/AY.132_and_AY.63/proportion_50_50

The file size of the simulated reads is too large to be uploaded on GitHub. We have made them available in this drive for your reference.