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seismic sim
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Purpose
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``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
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Run ``seismic sim {subcommand} --help`` for each subcommand's full option list.

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Subcommand    Description
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``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
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Quick example
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Run a full end-to-end simulation::

    seismic sim total --help

See the auto-generated :doc:`/cli` for the full option list for each subcommand.


See also
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- :doc:`/use/workflow/idmut` — the step whose output ``sim idmut`` mimics
- :doc:`/algos/index` — the underlying mutation models