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maxbin2-software

MaxBin2

MaxBin2 is the next-generation of MaxBin that supports multiple samples at the same time. MaxBin is a software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users could understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic sequences and the reads coverage information or sequencing reads.

Information

Usage

See versions of maxbin2 which are available:

$ module avail maxbin2

Load one version into your environment and run it:

$ module load maxbin2/2.2.7
$ run_MaxBin.pl

Note: Please use the -thread option to match the number of CPU threads requested in your SBATCH job parameters (default 1).

Installation

Notes from the sysadmin during installation:

$ cd /tmp
$ wget 'https://downloads.sourceforge.net/project/maxbin2/MaxBin-2.2.7.tar.gz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fmaxbin2%2Ffiles%2Flatest%2Fdownload&ts=1584261396' -O MaxBin-2.2.7.tar.gz
$ tar xf MaxBin-2.2.7.tar.gz 
$ cd MaxBin-2.2.7/src
$ scl enable devtoolset-7 bash
$ make
$ sed run_MaxBin.pl -i \
  -e 's/idba_ud/idba_hybrid/' \
  -e 's_IDBA\\-UD_IDBA\\-Hybrid_'
$ rm src/*.o
$ sudo cp -r *.hmm *.pl *.r src /export/apps/maxbin2/2.2.7
$ sudo chown -R root:root /export/apps/maxbin2/2.2.7

Note: according to the readme MaxBin2 needs IDBA-UD v1.1.1, but this version was published at least six years ago, after which time the binary was renamed to idba_hybrid. Old tarballs are not available so I will try to see if patching run_MaxBin.pl to use the new idba_hybrid binary works…

maxbin2-software.txt · Last modified: 2020/03/15 13:42 by aorth