seismic sim

Purpose

seismic sim generates synthetic sequencing data for testing and benchmarking. It is a group of subcommands that simulate individual components of the pipeline (reference sequences, structures, mutation rates, reads) or complete datasets.

Subcommands

Run seismic sim {subcommand} --help for each subcommand’s full option list.

Subcommand	Description
`ref`	Simulate a random reference sequence
`fold`	Simulate an RNA secondary structure
`params`	Simulate mutation-rate parameters for clusters
`clusts`	Simulate cluster memberships for reads
`ends`	Simulate read end positions
`muts`	Simulate per-read, per-position mutations
`idmut`	Simulate IDmut batch output directly
`fastq`	Simulate a FASTQ file from a reference
`total`	Run a full end-to-end simulation
`abstract`	Simulate abstract mutational data

Quick example

Run a full end-to-end simulation:

seismic sim total --help

See the auto-generated Command Line Reference for the full option list for each subcommand.

See also

seismic idmut — the step whose output sim idmut mimics
Algorithms — the underlying mutation models