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Disk-based k-mer counting (--kmc)

Myloasm's default k-mer counter holds everything in memory. For large or high-diversity metagenomes (e.g. soil, sediment) this can become the bottleneck. --kmc counts k-mers on disk instead, using a separate helper binary. --kmc is also usually faster than the default k-mer counter.

See the myloasm-kmc repo for install instructions and details.

Installation

Requirements: very standard unix-based toolchain (should be available by default) + the Rust language. Specifically,

  • a C++14 compiler (GCC 5+ or Clang)
  • zlib.h - zlib library installed
  • Rust programming language with cargo and associated tools installed.

Commands

git clone https://github.com/bluenote-1577/myloasm-kmc.git
cd myloasm-kmc
cargo install --path . # installs myloasm-kmc-v1 into ~/.cargo/bin

myloasm-kmc-v1 --help

myloasm-kmc-v1 should be in your PATH after this. It must be in PATH for the --kmc option to work.