mmlong

A collection of scripts for metagenome assembly using long reads.

Installation

Clone from github

Go to desired installation folder, open a terminal and run commands:
git clone https://github.com/SorenKarst/mmlong.git

Make bash scripts executable

Go to mmlong folder, open a terminal and run commands:
find . -name "mmlong*" -exec chmod +x {} ;

Create symlink to run mmlong from terminal

Open terminal and run command:
ln -s /path/to/mmlong/mmlong.sh /usr/local/bin
Test symlink by opening a terminal window anywhere
Type mmlong -h

Change paths to dependencies

Go to /path/to/mmlong/mmlong_tools and open dependencies.sh in a texteditor.
Change all paths under "Paths to dependencies" to reflect installations on you system.
If unsure of the paths try to type which <function> in the terminal. I.e. which racon.

Running mmlong functions

Accessing master script and tools

mmlong -h gives an overview of available tools.
mmlong <tool name> -h gives the help text for the specific tool. i.e. mmlong hybrid-metalflow

Example commands

mmlong hybrid-metaflow -d data -n np_asmb.txt -m np_cov.txt -s ilm_asmb.txt -i ilm_cov.txt -t 10 -l 4000 -k