karlon27/maxbin repository overview

=== Introduction === MaxBin is a software for binning assembled metagenomic contigs or scaffolds into distinct genomes. The software is available at https://sourceforge.net/projects/maxbin/⁠.

(It is also available at the JBEI MaxBin download server; however for weird reason the http site cannot be displayed correctly here in the Docker description. Please refer to the above sourceforge site and look for the JBEI download site.)

=== Parameters for running MaxBin Docker image === To run MaxBin Docker image on your dataset, you first need to place all necessary files into a folder and instruct Docker to link the folder. The command is

docker run -v (folder on local machine):/binning:rw karlon27/maxbin (additional MaxBin parameters)

For example, assume you want to run the 20X simulated metagenome using MaxBin Docker image. Here are the steps.

1. Download 20x.scaffold and 20x.abund from JBEI MaxBin download server (referred above).
2. Place them in /home/test/docker_test (this is a randomly made-up directory).
3. Invoke Docker command: docker run -v /home/test/docker_test:/binning:rw -w /binning karlon27/maxbin -contig 20x.scaffold -abund 20x.abund -out 20x.out -thread 4

In some cases, you need to set the directory into 0777 mode. Please try opening up the directory permission if you run into trouble.

Finally please refer to the MaxBin README file on JBEI download server (referred above) for MaxBin parameter descriptions.

=== Citation === Please cite the following article if you used MaxBin for binning your metagenome. Wu YW, Tang YH, Tringe SG, Simmons BA, and Singer SW, "MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm", Microbiome, 2:26, 2014.