KMC

KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files.

• Version: 3.1.1
• Added: November, 2018
• Updated: January, 2021
• Link: https://github.com/refresh-bio/KMC

See versions of kmc which are available:

$ module avail kmc

Load one version into your environment and run it:

$ module load kmc/3.1.1
$ kmc

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/refresh-bio/KMC/archive/v3.1.1.tar.gz
$ tar xf v3.1.1.tar.gz
$ cd KMC-3.1.1
# Install a newer compiler for C++14 features in KMC
$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++
$ scl enable devtoolset-7 bash
$ make
$ sudo mkdir -p /export/apps/kmc/3.1.1/bin
$ sudo cp bin/* /export/apps/kmc/3.1.1/bin