Simulates reads from ribosomal RNA contigs
Uses (NEAT GenReads)[https://github.com/zstephens/neat-genreads] to simulate sequencing of ribosomal genes. Currently it only simulates DNA. It can simulate the T2T sample or a fully synthetic sample in which the ribosomal gene contigs are taken from a synthetic catalogue of morphs, each generated from one of the 24 unique morphs found in the T2T with a random set of mutations. The mutations used for the synthetic catalogue for a randomly generated catalogue that is used by each synthetic morph to pick a random subset; this way morphs can share mutations across them
Creates a catalogue of mutations that will be incorporated into the different synthetic morphs
The mutations are listed with padding around them, instead of by position, so that the same mutation may be applied to slightly different morph templates.
Generate the morph catalogue to be used in simulating the sample FASTA
Uses a collection of template morphs and generates a new morph catalogue by taking random morphs from the reference catalogue and introducing randomly mutations from the mutation catalogue
Simulate a FASTA file
The file consists of a number of contigs formed by taking morphs from the catalogue with replacement
Simulates sequencing reads from a sample FASTA
Simulates sequencing reads from a cohort of samples