Installation

For Linux users, the easiest way to install MetaCortex is via Conda:

conda install -c bioconda metacortex

This will install MetaCortex with a maximum kmer size of 127.

For all other users (or to change the maximum kmer size), MetaCortex can be installed by compiling the source code with GCC. On the command line, first clone the GitHub repository and change the working directory with the following commands:

git clone https://github.com/SR-Martin/metacortex.git
cd metacortex

Next, compile the code. A decision needs to be made at compile-time on the largest k-mer size which you wish a given executable to support and this value may be either 31, 63, 95, 127, 160 or 192 nucleotides. Selecting this at compile-time allows for much more efficient use of memory during program execution. Often users will compile a number of different versions of the code, selecting at run-time the most appropriate one to use. The maximum kmer size may be specified as a parameter to the make command:

make MAXK=63 metacortex

When the build process completes, the executable may be found in the bin directory as metacortex_kX where X is the maximum kmer size chosen. To run MetaCortex, type e.g.:

./bin/metacortex_k63

Mac OS

Mac users will find that LLVM will not compile MetaCortex, so they will also need to install GCC, and set CC to point to the GCC binary before compiling:

export CC=/usr/local/bin/gcc-11

Then, compile the code with:

make MAXK=63 MAC=1 metacortex