How to install MOCAT2?

1. Download MOCAT2.
2. Extract it: $ unzip
3.Run the setup: $ perl
4. Load the into your $PATH-variable: $ source ~/.bashrc
5. Run MOCAT: $

NOTE: It may be that to run MOCAT you may need ot install the Perl5 File::Sync library: $ perl -MCPAN -e shell (and then: install File::Sync)
MOCAT2 requires Perl 5.16+ and Python 2.6.6+.

Download MOCAT2 & Databases

Do you want the absolutely latest developement version of MOCAT2?
Visit the MOCAT2 github page

Do you want the public, stable version of MOCAT2?
Download MOCAT2 v 2.0 (4 GB) | Manual in PDF format
Why is the download 4.0 GB large? Because it includes the eggNOG database for functional annotations, pre-calculated alignmnts to other databases and example files

Do you want the public, stable version of MOCAT2 WITHOUT functional annotation capabilities?
Download MOCAT2 v 2.0 (26 MB) | Manual in PDF format

Do you want a Linux virtual machine that has been tested to run MOCAT?
We recommend using Bio-Linux v8

Pre-compiled reference gene catalogs (RGCs) for funcitonal profiling:
Downloads include (padded) nucleotide sequences, required coord and length files, and functional annotation file = all you'd ever need ;)
IGC (human gut): Download (2.6 GB) | Reference
Colorectal cancer-RGC (human gut): Download (2.2 GB) | Reference
skin-RGC (human skin): Download (1.1 GB) | Reference
mouse-RGC (mouse gut): Download (0.7 GB) | Reference
OM-RGC (ocean): Download (9.3 GB) | Reference

Databases for MOCAT2:
Taxonomic profiling (these are included in the MOCAT2 download already):
RefMG.v1 database (summarizing into specI & NCBI taxonomic levels)
mOTU.v1 database (summarizing into mOTU-LGs)
Human reference genome (not included in the MOCAT2 download):
Human Genome 19 database (used for removing human contaminants)

Example datasets and the datasets used in the article are here (these can be automatically downloaded when installing MOCAT2):
Download HMP mock community reference genomes (from MOCAT article; 35 MB)
Download HMP mock community metagenome (from MOCAT article; 500 MB)
Download 100 simulated reference strains (from MOCAT article; 110 MB)
Download simulated metagenome (100 strains) (from MOCAT article; 3.3 GB)
Download simulated metagenome (87 species) (from mOTU article; 2.1 GB)

Do you want to use an older version of MOCAT?
Download MOCAT v1.3 | Manual in PDF format
Download MOCAT v1.1 | Manual in PDF format
Download MOCAT v1.0 | Manual in PDF format

Do you want to download the Virtual Machine (VM) with MOCAT v1.1 (not the latest MOCAT version)?
The VM enables users to run MOCAT within a UNIX environment on for example a PC, Mac or in a local or public cloud system. To setup and run the VM, you will need to install either VMWare Player (for PC) or VMWare Fusion (for Mac). After installing the VMWare software, launch the VM and login with username 'ubuntu' and password 'ubuntu'. MOCAT can then easily be setup bu extracting the MOCATv1.1.tar file by executing 'tar -xvf MOCATv1.1.tar'. We have chosen to not fully install MOCAT, because the user has to selecte the number of CPUs on the current system during the installation. Furthermore we recommend installing and running MOCAT on a partition (HDD) outside of the VM by enabling sharing inside the VMWare package.
Download the VM with MOCAT v1.1 (4.0 GB)