Quick Start - vikshiv/mumemto GitHub Wiki

Installation

## Install from source with pip
git clone https://github.com/vshiv18/mumemto
pip install .

# OR install from bioconda
conda install -c bioconda mumemto

See Installation for more details.

Running Mumemto

The basic command to run mumemto is

mumemto *.fa -o <output-prefix>

This will pass in the specified FASTA files and build three output files starting with the output prefix:

• prefix.mums: the location of multi-MUMs across all the input sequences
• prefix.lengths: a list of input file paths and the length of each sequence

See Input and Output formats for more information on the input and output formats.

A full list of subcommands is available by running mumemto without any additional parameters, and additional parameters for the main mumemto command are available with mumemto -h. Additionally, see the relevant wiki pages for more information.

Visualize multi-MUM synteny

The viz module can visualize multi-MUM synteny blocks from the output of mumemto

mumemto viz -i <output-prefix>

See Visualization for more usage information.