Markov genome

Model a sequence database as a Markov process of order n and simulate random sequences with a similar k-mer count distribution. Markov genome ignores case and can model arbitrary 8-bit alphabets.

Download and Installation

Install with cargo (Linux)

cargo install markov_genome

Install with bioconda (Linux)

conda install -c bioconda -c conda-forge markov_genome

Build from source

Prerequisites

• Rust >= 1.74
• git

Refer to the Rust Setup Tutorial for more in depth information.

Download current master branch

git clone git@github.com:eaasna/markov_genome.git

Building

cd markov_genome
cargo build --release

The markov_genome binary can be found in target/release/.

You may want to add the executable to your PATH:

export PATH=$(pwd)/target/release/markov_genome:$PATH
markov_genome --help

Sequence simulation

Learn the transition probabilities of the test reference database and use a Markov process of order 3 to simulate two chromosomes of length 100bp:

markov_genome --input test/ref.fasta --output sim.fasta --order 3 --lens 100 --lens 100

For a detailed list of options, see the help page:

markov_genome --help