MAXBIN
MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. MaxBin shows the underlying bins (genomes) of the microbes in their metagenomes from assembled metagenomic sequences and the reads coverage information or sequencing reads. MaxBin will report genome-related statistics, including estimated completeness, GC content and genome size in the binning summary page.
MEGAN can be used on MaxBin bins to find the taxonomy of each bin after the binning process is finished.
Documentation
- MaxBin web site
- 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.
- Wu YW, Simmons BA, and Singer SW, "MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets", Bioinformatics, 32(4): 605-607, 2016.
Usage
To see what versions of MaxBin are available type
module avail maxbin
To see what other modules are needed, what commands are available and how to get additional help type
module help maxbin
To use MaxBin, include a command like this in your batch script to load the Maxbin module:
module load maxbin
Be sure you also load any other modules needed, as listed by the module help maxbin command.