                                    Mason
                   Tools for Biological Sequence Simulation

                      http://www.seqan.de/projects/mason
                             Version 2.0.0alpha2
                                October, 2013

                               Manuel Holtgrewe

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Table of Contents
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  1. Overview

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1. Overview
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Mason is a collection of tools for the simulation of biological sequences.
The collection consists of the following tools.  For each tool, there is file
README.${tool_name} that contains detailed documentation of the tool itself.
Also you can get detailed documentation of a tool's parameters by calling it
with the "--help" argument.

 * mason_genome
       Simulation of random genomic sequences.
 * mason_variator
       Simulate SNPs, small indels, and structural variants for genomic data.
       The result is written out as a VCF file.  Optionally, the resulting
       modified sequence can also be written out.
 * mason_materializer
       Apply the variation from a VCF file to a genome in a FASTA file.
 * mason_methylation
       Simulate methylation levels for a genome dependent on the context for
       each possible site.
 * mason_simulator
       Simulate NGS reads given a genome and optionally also a VCF file with
       variants for a given donor to use as the source.
 * mason_splicing
       Compute the transcriptome from a genome FASTA file and a GFF file with
       the genes.
 * mason_frag_sequencing
       Simulation of fragment sampling from a genome.
